ijms-logo

Journal Browser

Journal Browser

Advances in Molecular Simulation

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (30 September 2021) | Viewed by 45806

Printed Edition Available!
A printed edition of this Special Issue is available here.

Special Issue Editor

Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie-Skłodowska University in Lublin, 20-031 Lublin, Poland
Interests: molecular simulations; theory of fluids; interfacial phenomena; phase transitions; Janus particles; hairy nanoparticles; chromatography
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Molecular simulations play an increasingly significant role in science today. The rapid progress in computer technology has given a strong impetus to the development of many statistical–mechanical methods for modeling physical, chemical and biological processes. Among the simulation techniques, molecular dynamics and the Monte Carlo method are the most popular. The simulations provide a tool which allows for interpolation between laboratory experiments and theory, and for a deeper insight into the processes being studied when direct measurements are not possible.  

We are currently observing the explosive development of simulation methods and their applications in fundamental and technological research. The latter range from the design of new smart materials, active materials, through the development of drugs and drug delivery to the fabrication of novel biomaterials for DNA sequencing, and many others.

 This Special Issue collects papers devoted to the extension of novel simulation techniques and new methods for the analysis of the results. The other aim is to present applications of computer simulations to explore different phenomena with a focus on the explanation of their molecular mechanism and on the description of potential practical applications in nanotechnology, biotechnology, and medicine.

Prof. Dr. Małgorzata Borówko
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • molecular simulation
  • molecular dynamics
  • Monte Carlo method
  • molecular modeling
  • self-assembly
  • phase transitions
  • nanoparticles
  • supramolecular structures
  • biotechnology
  • nanotechnology

Related Special Issues

Published Papers (16 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Editorial

Jump to: Research, Review

3 pages, 151 KiB  
Editorial
Special Issue on Advances in Molecular Simulation
by Małgorzta Borówko
Int. J. Mol. Sci. 2021, 22(22), 12484; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212484 - 19 Nov 2021
Cited by 1 | Viewed by 1346
Abstract
Rapid advances are taking place in the application of molecular simulations to study complex systems [...] Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)

Research

Jump to: Editorial, Review

25 pages, 13052 KiB  
Article
Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions
by Miguel Herranz, Daniel Martínez-Fernández, Pablo Miguel Ramos, Katerina Foteinopoulou, Nikos Ch. Karayiannis and Manuel Laso
Int. J. Mol. Sci. 2021, 22(22), 12464; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222212464 - 18 Nov 2021
Cited by 7 | Viewed by 1743
Abstract
We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, [...] Read more.
We present Simu-D, a software suite for the simulation and successive identification of local structures of atomistic systems, based on polymers, under extreme conditions, in the bulk, on surfaces, and at interfaces. The protocol is built around various types of Monte Carlo algorithms, which include localized, chain-connectivity-altering, identity-exchange, and cluster-based moves. The approach focuses on alleviating one of the main disadvantages of Monte Carlo algorithms, which is the general applicability under a wide range of conditions. Present applications include polymer-based nanocomposites with nanofillers in the form of cylinders and spheres of varied concentration and size, extremely confined and maximally packed assemblies in two and three dimensions, and terminally grafted macromolecules. The main simulator is accompanied by a descriptor that identifies the similarity of computer-generated configurations with respect to reference crystals in two or three dimensions. The Simu-D simulator-descriptor can be an especially useful tool in the modeling studies of the entropy- and energy-driven phase transition, adsorption, and self-organization of polymer-based systems under a variety of conditions. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Graphical abstract

17 pages, 4217 KiB  
Article
Structural and Dynamical Behaviour of Colloids with Competing Interactions Confined in Slit Pores
by Horacio Serna, Wojciech T. Góźdź and Eva G. Noya
Int. J. Mol. Sci. 2021, 22(20), 11050; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222011050 - 13 Oct 2021
Cited by 3 | Viewed by 1596
Abstract
Systems with short-range attractive and long-range repulsive interactions can form periodic modulated phases at low temperatures, such as cluster-crystal, hexagonal, lamellar and bicontinuous gyroid phases. These periodic microphases should be stable regardless of the physical origin of the interactions. However, they have not [...] Read more.
Systems with short-range attractive and long-range repulsive interactions can form periodic modulated phases at low temperatures, such as cluster-crystal, hexagonal, lamellar and bicontinuous gyroid phases. These periodic microphases should be stable regardless of the physical origin of the interactions. However, they have not yet been experimentally observed in colloidal systems, where, in principle, the interactions can be tuned by modifying the colloidal solution. Our goal is to investigate whether the formation of some of these periodic microphases can be promoted by confinement in narrow slit pores. By performing simulations of a simple model with competing interactions, we find that both the cluster-crystal and lamellar phases can be stable up to higher temperatures than in the bulk system, whereas the hexagonal phase is destabilised at temperatures somewhat lower than in bulk. Besides, we observed that the internal ordering of the lamellar phase can be modified by changing the pore width. Interestingly, for sufficiently wide pores to host three lamellae, there is a range of temperatures for which the two lamellae close to the walls are internally ordered, whereas the one at the centre of the pore remains internally disordered. We also find that particle diffusion under confinement exhibits a complex dependence with the pore width and with the density, obtaining larger and smaller values of the diffusion coefficient than in the corresponding bulk system. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

16 pages, 5353 KiB  
Article
A Systematic Approach: Molecular Dynamics Study and Parametrisation of Gemini Type Cationic Surfactants
by Mateusz Rzycki, Aleksandra Kaczorowska, Sebastian Kraszewski and Dominik Drabik
Int. J. Mol. Sci. 2021, 22(20), 10939; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222010939 - 10 Oct 2021
Cited by 3 | Viewed by 1986
Abstract
The spreading of antibiotic-resistant bacteria strains is one of the most serious problem in medicine to struggle nowadays. This triggered the development of alternative antimicrobial agents in recent years. One of such group is Gemini surfactants which are massively synthesised in various structural [...] Read more.
The spreading of antibiotic-resistant bacteria strains is one of the most serious problem in medicine to struggle nowadays. This triggered the development of alternative antimicrobial agents in recent years. One of such group is Gemini surfactants which are massively synthesised in various structural configurations to obtain the most effective antibacterial properties. Unfortunately, the comparison of antimicrobial effectiveness among different types of Gemini agents is unfeasible since various protocols for the determination of Minimum Inhibitory Concentration are used. In this work, we proposed alternative, computational, approach for such comparison. We designed a comprehensive database of 250 Gemini surfactants. Description of structure parameters, for instance spacer type and length, are included in the database. We parametrised modelled molecules to obtain force fields for the entire Gemini database. This was used to conduct in silico studies using the molecular dynamics to investigate the incorporation of these agents into model E. coli inner membrane system. We evaluated the effect of Gemini surfactants on structural, stress and mechanical parameters of the membrane after the agent incorporation. This enabled us to select four most likely membrane properties that could correspond to Gemini’s antimicrobial effect. Based on our results we selected several types of Gemini spacers which could demonstrate a particularly strong effect on the bacterial membranes. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

18 pages, 1359 KiB  
Article
Phase Transitions in Two-Dimensional Systems of Janus-like Particles on a Triangular Lattice
by Andrzej Patrykiejew
Int. J. Mol. Sci. 2021, 22(19), 10484; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910484 - 28 Sep 2021
Viewed by 1180
Abstract
We studied the phase behavior of two-dimensional systems of Janus-like particles on a triangular lattice using Monte Carlo methods. The model assumes that each particle can take on one of the six orientations with respect to the lattice, and the interactions between neighboring [...] Read more.
We studied the phase behavior of two-dimensional systems of Janus-like particles on a triangular lattice using Monte Carlo methods. The model assumes that each particle can take on one of the six orientations with respect to the lattice, and the interactions between neighboring particles were weighted depending on the degree to which their A and B halves overlap. In this work, we assumed that the AA interaction was fixed and attractive, while the AB and BB interactions varied. We demonstrated that the phase behavior of the systems considered strongly depended on the magnitude of the interaction energies between the AB and BB halves. Here, we considered systems with non-repulsive interactions only and determined phase diagrams for several systems. We demonstrated that the phase diagram topology depends on the temperature at which the close-packed systems undergo the orientational order–disorder transition. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

16 pages, 1939 KiB  
Article
Can We Predict the Isosymmetric Phase Transition? Application of DFT Calculations to Study the Pressure Induced Transformation of Chlorothiazide
by Łukasz Szeleszczuk, Anna Helena Mazurek, Katarzyna Milcarz, Ewa Napiórkowska and Dariusz Maciej Pisklak
Int. J. Mol. Sci. 2021, 22(18), 10100; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221810100 - 18 Sep 2021
Cited by 4 | Viewed by 2430
Abstract
Isosymmetric structural phase transition (IPT, type 0), in which there are no changes in the occupation of Wyckoff positions, the number of atoms in the unit cell, and the space group symmetry, is relatively uncommon. Chlorothiazide, a diuretic agent with a secondary function [...] Read more.
Isosymmetric structural phase transition (IPT, type 0), in which there are no changes in the occupation of Wyckoff positions, the number of atoms in the unit cell, and the space group symmetry, is relatively uncommon. Chlorothiazide, a diuretic agent with a secondary function as an antihypertensive, has been proven to undergo pressure-induced IPT of Form I to Form II at 4.2 GPa. For that reason, it has been chosen as a model compound in this study to determine if IPT can be predicted in silico using periodic DFT calculations. The transformation of Form II into Form I, occurring under decompression, was observed in geometry optimization calculations. However, the reverse transition was not detected, although the calculated differences in the DFT energies and thermodynamic parameters indicated that Form II should be more stable at increased pressure. Finally, the IPT was successfully simulated using ab initio molecular dynamics calculations. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

13 pages, 2120 KiB  
Article
Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations
by Bilal Ahmad, Maria Batool, Qurat ul Ain, Moon Suk Kim and Sangdun Choi
Int. J. Mol. Sci. 2021, 22(17), 9124; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22179124 - 24 Aug 2021
Cited by 77 | Viewed by 10745
Abstract
The novel coronavirus disease, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), rapidly spreading around the world, poses a major threat to the global public health. Herein, we demonstrated the binding mechanism of PF-07321332, α-ketoamide, lopinavir, and ritonavir to the coronavirus 3-chymotrypsin-like-protease (3CL [...] Read more.
The novel coronavirus disease, caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), rapidly spreading around the world, poses a major threat to the global public health. Herein, we demonstrated the binding mechanism of PF-07321332, α-ketoamide, lopinavir, and ritonavir to the coronavirus 3-chymotrypsin-like-protease (3CLpro) by means of docking and molecular dynamic (MD) simulations. The analysis of MD trajectories of 3CLpro with PF-07321332, α-ketoamide, lopinavir, and ritonavir revealed that 3CLpro–PF-07321332 and 3CLpro–α-ketoamide complexes remained stable compared with 3CLpro–ritonavir and 3CLpro–lopinavir. Investigating the dynamic behavior of ligand–protein interaction, ligands PF-07321332 and α-ketoamide showed stronger bonding via making interactions with catalytic dyad residues His41–Cys145 of 3CLpro. Lopinavir and ritonavir were unable to disrupt the catalytic dyad, as illustrated by increased bond length during the MD simulation. To decipher the ligand binding mode and affinity, ligand interactions with SARS-CoV-2 proteases and binding energy were calculated. The binding energy of the bespoke antiviral PF-07321332 clinical candidate was two times higher than that of α-ketoamide and three times than that of lopinavir and ritonavir. Our study elucidated in detail the binding mechanism of the potent PF-07321332 to 3CLpro along with the low potency of lopinavir and ritonavir due to weak binding affinity demonstrated by the binding energy data. This study will be helpful for the development and optimization of more specific compounds to combat coronavirus disease. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

21 pages, 18290 KiB  
Article
Adsorption on Ligand-Tethered Nanoparticles
by Małgorzata Borówko and Tomasz Staszewski
Int. J. Mol. Sci. 2021, 22(16), 8810; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22168810 - 16 Aug 2021
Cited by 6 | Viewed by 1699
Abstract
We use coarse-grained molecular dynamics simulations to study adsorption on ligand-tethered particles. Nanoparticles with attached flexible and stiff ligands are considered. We discuss how the excess adsorption isotherm, the thickness of the polymer corona, and its morphology depend on the number of ligands, [...] Read more.
We use coarse-grained molecular dynamics simulations to study adsorption on ligand-tethered particles. Nanoparticles with attached flexible and stiff ligands are considered. We discuss how the excess adsorption isotherm, the thickness of the polymer corona, and its morphology depend on the number of ligands, their length, the size of the core, and the interaction parameters. We investigate the adsorption-induced structural transitions of polymer coatings. The behavior of systems involving curved and flat “brushes” is compared. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

12 pages, 1021 KiB  
Article
Time-Dependent Unitary Transformation Method in the Strong-Field-Ionization Regime with the Kramers-Henneberger Picture
by Je-Hoi Mun, Hirofumi Sakai and Dong-Eon Kim
Int. J. Mol. Sci. 2021, 22(16), 8514; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22168514 - 07 Aug 2021
Cited by 1 | Viewed by 1882
Abstract
Time evolution operators of a strongly ionizing medium are calculated by a time-dependent unitary transformation (TDUT) method. The TDUT method has been employed in a quantum mechanical system composed of discrete states. This method is especially helpful for solving molecular rotational dynamics in [...] Read more.
Time evolution operators of a strongly ionizing medium are calculated by a time-dependent unitary transformation (TDUT) method. The TDUT method has been employed in a quantum mechanical system composed of discrete states. This method is especially helpful for solving molecular rotational dynamics in quasi-adiabatic regimes because the strict unitary nature of the propagation operator allows us to set the temporal step size to large; a tight limitation on the temporal step size (δt<<1) can be circumvented by the strict unitary nature. On the other hand, in a strongly ionizing system where the Hamiltonian is not Hermitian, the same approach cannot be directly applied because it is demanding to define a set of field-dressed eigenstates. In this study, the TDUT method was applied to the ionizing regime using the Kramers-Henneberger frame, in which the strong-field-dressed discrete eigenstates are given by the field-free discrete eigenstates in a moving frame. Although the present work verifies the method for a one-dimensional atom as a prototype, the method can be applied to three-dimensional atoms, and molecules exposed to strong laser fields. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

11 pages, 3648 KiB  
Article
Molecular Insight into the Possible Mechanism of Drag Reduction of Surfactant Aqueous Solution in Pipe Flow
by Yusei Kobayashi, Hirotaka Gomyo and Noriyoshi Arai
Int. J. Mol. Sci. 2021, 22(14), 7573; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22147573 - 15 Jul 2021
Cited by 8 | Viewed by 1973
Abstract
The phenomenon of drag reduction (known as the “Toms effect”) has many industrial and engineering applications, but a definitive molecular-level theory has not yet been constructed. This is due both to the multiscale nature of complex fluids and to the difficulty of directly [...] Read more.
The phenomenon of drag reduction (known as the “Toms effect”) has many industrial and engineering applications, but a definitive molecular-level theory has not yet been constructed. This is due both to the multiscale nature of complex fluids and to the difficulty of directly observing self-assembled structures in nonequilibrium states. On the basis of a large-scale coarse-grained molecular simulation that we conducted, we propose a possible mechanism of turbulence suppression in surfactant aqueous solution. We demonstrate that maintaining sufficiently large micellar structures and a homogeneous radial distribution of surfactant molecules is necessary to obtain the drag-reduction effect. This is the first molecular-simulation evidence that a micellar structure is responsible for drag reduction in pipe flow, and should help in understanding the mechanisms underlying drag reduction by surfactant molecules under nonequilibrium conditions. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

22 pages, 4803 KiB  
Article
Recent Developments on gMicroMC: Transport Simulations of Proton and Heavy Ions and Concurrent Transport of Radicals and DNA
by Youfang Lai, Xun Jia and Yujie Chi
Int. J. Mol. Sci. 2021, 22(12), 6615; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22126615 - 21 Jun 2021
Cited by 5 | Viewed by 2088
Abstract
Mechanistic Monte Carlo (MC) simulation of radiation interaction with water and DNA is important for the understanding of biological responses induced by ionizing radiation. In our previous work, we employed the Graphical Processing Unit (GPU)-based parallel computing technique to develop a novel, highly [...] Read more.
Mechanistic Monte Carlo (MC) simulation of radiation interaction with water and DNA is important for the understanding of biological responses induced by ionizing radiation. In our previous work, we employed the Graphical Processing Unit (GPU)-based parallel computing technique to develop a novel, highly efficient, and open-source MC simulation tool, gMicroMC, for simulating electron-induced DNA damages. In this work, we reported two new developments in gMicroMC: the transport simulation of protons and heavy ions and the concurrent transport of radicals in the presence of DNA. We modeled these transports based on electromagnetic interactions between charged particles and water molecules and the chemical reactions between radicals and DNA molecules. Various physical properties, such as Linear Energy Transfer (LET) and particle range, from our simulation agreed with data published by NIST or simulation results from other CPU-based MC packages. The simulation results of DNA damage under the concurrent transport of radicals and DNA agreed with those from nBio-Topas simulation in a comprehensive testing case. GPU parallel computing enabled high computational efficiency. It took 41 s to simultaneously transport 100 protons with an initial kinetic energy of 10 MeV in water and 470 s to transport 105 radicals up to 1 µs in the presence of DNA. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

17 pages, 2473 KiB  
Article
Computational-Driven Epitope Verification and Affinity Maturation of TLR4-Targeting Antibodies
by Bilal Ahmad, Maria Batool, Moon-Suk Kim and Sangdun Choi
Int. J. Mol. Sci. 2021, 22(11), 5989; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22115989 - 01 Jun 2021
Cited by 6 | Viewed by 2860
Abstract
Toll-like receptor (TLR) signaling plays a critical role in the induction and progression of autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematous, experimental autoimmune encephalitis, type 1 diabetes mellitus and neurodegenerative diseases. Deciphering antigen recognition by antibodies provides insights and defines the [...] Read more.
Toll-like receptor (TLR) signaling plays a critical role in the induction and progression of autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematous, experimental autoimmune encephalitis, type 1 diabetes mellitus and neurodegenerative diseases. Deciphering antigen recognition by antibodies provides insights and defines the mechanism of action into the progression of immune responses. Multiple strategies, including phage display and hybridoma technologies, have been used to enhance the affinity of antibodies for their respective epitopes. Here, we investigate the TLR4 antibody-binding epitope by computational-driven approach. We demonstrate that three important residues, i.e., Y328, N329, and K349 of TLR4 antibody binding epitope identified upon in silico mutagenesis, affect not only the interaction and binding affinity of antibody but also influence the structural integrity of TLR4. Furthermore, we predict a novel epitope at the TLR4-MD2 interface which can be targeted and explored for therapeutic antibodies and small molecules. This technique provides an in-depth insight into antibody–antigen interactions at the resolution and will be beneficial for the development of new monoclonal antibodies. Computational techniques, if coupled with experimental methods, will shorten the duration of rational design and development of antibody therapeutics. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

19 pages, 29719 KiB  
Article
Simple Models to Study Spectral Properties of Microbial and Animal Rhodopsins: Evaluation of the Electrostatic Effect of Charged and Polar Residues on the First Absorption Band Maxima
by Andrey A. Shtyrov, Dmitrii M. Nikolaev, Vladimir N. Mironov, Andrey V. Vasin, Maxim S. Panov, Yuri S. Tveryanovich and Mikhail N. Ryazantsev
Int. J. Mol. Sci. 2021, 22(6), 3029; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22063029 - 16 Mar 2021
Cited by 9 | Viewed by 2737
Abstract
A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum [...] Read more.
A typical feature of proteins from the rhodopsin family is the sensitivity of their absorption band maximum to protein amino acid composition. For this reason, studies of these proteins often require methodologies that determine spectral shift caused by amino acid substitutions. Generally, quantum mechanics/molecular mechanics models allow for the calculation of a substitution-induced spectral shift with high accuracy, but their application is not always easy and requires special knowledge. In the present study, we propose simple models that allow us to estimate the direct effect of a charged or polar residue substitution without extensive calculations using only rhodopsin three-dimensional structure and plots or tables that are provided in this article. The models are based on absorption maximum values calculated at the SORCI+Q level of theory for cis- and trans-forms of retinal protonated Schiff base in an external electrostatic field of charges and dipoles. Each value corresponds to a certain position of a charged or polar residue relative to the retinal chromophore. The proposed approach was evaluated against an example set consisting of twelve bovine rhodopsin and sodium pumping rhodopsin mutants. The limits of the applicability of the models are also discussed. The results of our study can be useful for the interpretation of experimental data and for the rational design of rhodopsins with required spectral properties. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

24 pages, 65005 KiB  
Article
Osmosis-Driven Water Transport through a Nanochannel: A Molecular Dynamics Simulation Study
by Changsun Eun
Int. J. Mol. Sci. 2020, 21(21), 8030; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21218030 - 28 Oct 2020
Cited by 3 | Viewed by 2069
Abstract
In this work, we study a chemical method to transfer water molecules from a nanoscale compartment to another initially empty compartment through a nanochannel. Without any external force, water molecules do not spontaneously move to the empty compartment because of the energy barrier [...] Read more.
In this work, we study a chemical method to transfer water molecules from a nanoscale compartment to another initially empty compartment through a nanochannel. Without any external force, water molecules do not spontaneously move to the empty compartment because of the energy barrier for breaking water hydrogen bonds in the transport process and the attraction between water molecules and the compartment walls. To overcome the energy barrier, we put osmolytes into the empty compartment, and to remove the attraction, we weaken the compartment-water interaction. This allows water molecules to spontaneously move to the empty compartment. We find that the initiation and time-transient behavior of water transport depend on the properties of the osmolytes specified by their number and the strength of their interaction with water. Interestingly, when osmolytes strongly interact with water molecules, transport immediately starts and continues until all water molecules are transferred to the initially empty compartment. However, when the osmolyte interaction strength is intermediate, transport initiates stochastically, depending on the number of osmolytes. Surprisingly, because of strong water-water interactions, osmosis-driven water transport through a nanochannel is similar to pulling a string at a constant speed. Our study helps us understand what minimal conditions are needed for complete transfer of water molecules to another compartment through a nanochannel, which may be of general concern in many fields involving molecular transfer. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Graphical abstract

Review

Jump to: Editorial, Research

14 pages, 2262 KiB  
Review
Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory
by Dipankar Roy and Andriy Kovalenko
Int. J. Mol. Sci. 2021, 22(10), 5061; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22105061 - 11 May 2021
Cited by 9 | Viewed by 2572
Abstract
The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small [...] Read more.
The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé–Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

21 pages, 2426 KiB  
Review
“Dividing and Conquering” and “Caching” in Molecular Modeling
by Xiaoyong Cao and Pu Tian
Int. J. Mol. Sci. 2021, 22(9), 5053; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22095053 - 10 May 2021
Cited by 4 | Viewed by 3568
Abstract
Molecular modeling is widely utilized in subjects including but not limited to physics, chemistry, biology, materials science and engineering. Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been [...] Read more.
Molecular modeling is widely utilized in subjects including but not limited to physics, chemistry, biology, materials science and engineering. Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, most important methodological advancements in more than half century of molecular modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes “dividing and conquering” and/or “caching” in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but results are not transferable. Deep learning has been utilized to realize more efficient and accurate ways of “dividing and conquering” and “caching” along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science. This framework is based on a third class of algorithm that facilitates molecular modeling through partially transferable in resolution “caching” of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for “dividing and conquering” and “caching” in complex molecular systems. Full article
(This article belongs to the Special Issue Advances in Molecular Simulation)
Show Figures

Figure 1

Back to TopTop