Molecular Simulation

Article	Citations
A review of advancements in coarse-grained molecular dynamics simulations	104
Finite-size effects of diffusion coefficients computed from molecular dynamics: a review of what we have learned so far	89
COMPASS III: automated fitting workflows and extension to ionic liquids	80
RETRACTED ARTICLE: Ir-decorated gallium nitride nanotubes as a chemical sensor for recognition of mesalamine drug: a DFT study	64
Atomistica.online – web application for generating input files for ORCA molecular modelling package made with the Anvil platform	49
Recent advances in the continuous fractional component Monte Carlo methodology	39
Materials Studio 20th anniversary	36
The adsorption of chlorofluoromethane on pristine and Ge-doped silicon carbide nanotube: a PBC-DFT, NBO, and QTAIM study	34
Machine learning and descriptor selection for the computational discovery of metal-organic frameworks	29
Influence of NiO decoration on adsorption capabilities of black phosphorus monolayer toward nitrogen dioxide: periodic DFT calculations	27
Solvent-free grindstone synthesis of four new (E)-7-(arylidene)-indanones and their structural, spectroscopic and quantum chemical study: a comprehensive theoretical and experimental exploratio	26
Monte Carlo simulations of hydrogen adsorption in fullerene pillared graphene nanocomposites	22
T cell epitope designing for dengue peptide vaccine using docking and molecular simulation studies	21
Ab initio study of N-doped graphene oxide (NDGO) as a promising anode material for Li-ion rechargeable battery	20
In-silico strategies of some selected phytoconstituents from Melissa officinalis as SARS CoV-2 main protease and spike protein (COVID-19) inhibitors	19
A molecular docking and dynamic approach to screen inhibitors against ZnuA1 ofCandidatusLiberibacter asiaticus	18
Reactive molecular dynamics simulation on the structure characteristics and tensile properties of calcium silicate hydrate at various temperatures and strain rates	17
Molecular modelling framework of metal-organic clusters for conserving surfaces: Langmuir sorption through the TD-DFT/ONIOM approach	17
Dimethyl and ethyl methyl ether adsorption studies on β-antimonene nanosheets – a first-principles study	17
Fast transport of water in carbon nanotubes: a review of current accomplishments and challenges	17
Understanding the influence of single metal (Li, Mg, Al, Fe, Ag) doping on the electronic and optical properties of g-C3N4: a theoretical study	16
Study of the adsorption of chloropicrin on pure and Ga and Al doped B12N12: a comprehensive DFT and QTAIM investigation	16
Thermal conductivity and mechanical properties of graphene-like BC2, BC3 and B4C3	16
Adaptive steered molecular dynamics of biomolecules	16
PoreMS: a software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions	15

A synergic effect of CNT/Al2O3 reinforcements on multiscale epoxy-based glass fiber composite: fabrication and molecular dynamics modeling	15
Acetaminophen and mepirizole molecular adsorption studies on novel ζ – phosphorene nanotube based on first-principles investigation	14
Novel green phosphorene as a superior gas sensor for dissolved gas analysis in oil transformers: using DFT method	14
In silico toxicity investigation of Methaqualone’s conjunctival, retinal, and gastrointestinal hemorrhage by molecular modelling approach	14
Spectroscopic, quantum chemical and molecular docking studies on 2,4-dimethoxy-1,3,5-triazine: a potent inhibitor of protein kinase CK2 for the development of breast cancer drug	13
A study of the microscopic interaction mechanism of styrene–butadiene-styrene modified asphalt based on density functional theory	13
Molecular simulations of interfacial systems: challenges, applications and future perspectives	13
Compatibility and high temperature performance of recycled polyethylene modified asphalt using molecular simulations	13
Structural and vibrational spectral investigation on the identification of Non-Linear Optical properties and wave function analyses (electrostatic potential, electron localisation function, localised	12
Molecular modelling of antiproliferative inhibitors based on SMILES descriptors using Monte-Carlo method, docking, MD simulations and ADME/Tox studies	12
A modified many-body dissipative particle dynamics model for mesoscopic fluid simulation: methodology, calibration, and application for hydrocarbon and water	11
Theoretical studies of Thiazolyl-Pyrazoline derivatives as promising drugs against malaria by QSAR modelling combined with molecular docking and molecular dynamics simulation	11
Theoretical insights about inhibition efficiencies of some 8-Hydroxyqionoline derivatives against the corrosion of mild steel	11
Application of magnetic electrospun polyvinyl alcohol/collagen nanofibres for drug delivery systems	10
A ReaxFF molecular dynamics study on the mechanism and the typical pyrolysis gases in the pyrolysis process of Longkou oil shale kerogen	10
Index of ideality of correlation and correlation contradiction index: a confluent perusal on acetylcholinesterase inhibitors	10
An in silico molecular dynamics simulation study on the inhibitors of SARS-CoV-2 proteases (3CLpro and PLpro) to combat COVID-19	10
Computational investigations on efficient metal-free organic D-π-A dyes with different spacers for powerful DSSCs applications	9
Revealing the role of hydrogen bonding in polyurea with multiscale simulations	9
Study of the aggregation behaviour of three primary reactive dyes via molecular dynamics simulations	9
Effect of annealing temperature on photoluminescence spectra, gap states using different models and optical dispersion parameters in copper-doped ZnO films	9
Identification of promising compounds from curry tree with cyclooxygenase inhibitory potential using a combination of machine learning, molecular docking, dynamics simulations and binding free energy	9
Temperature and molecular crowding effects on the sensitivity of T30695 aptamer toward Pb2+ion: a joint molecular dynamics simulation and experimental study	9
Synthesis of 5, 6-diaroylisoindoline-1, 3-dione and computational approaches for investigation on structural and mechanistic insights by DFT	9
Temperature and its control in molecular dynamics simulations	9
Computational screening of metal–organic framework structures for separation of propane/propene mixture	9
Plant-based bioactive molecules for targeting of endoribonuclease using steered molecular dynamic simulation approach: a highly conserved therapeutic target against variants of SARS-CoV-2	9
Estimation of improvement in elastic moduli for functionalised defective graphene-based thermoplastic polyurethane nanocomposites: a molecular dynamics approach	9
Structural geometry, electronic structure, thermo-electronic and optical properties of GaCuO2 and GaCu0.94Fe0.06O2: a first principle approach of three DFT	8
Effects of Ag-decoration on the adsorption and detection of toxic OF2 gas on a GaN nanotube	8
Coadsorption of Na+ and H2O on the surface of hydroxylated silica	8
Potential antifungal activity of novel carbohydrate derivatives validated by POM, molecular docking and molecular dynamic simulations analyses	8
Computational binding study with α7 nicotinic acetylcholine receptor of Anvylic-3288: an allosteric modulator	8
The importance of reference frame for pressure at the liquid–vapour interface	8
Scaling for rectification of bipolar nanopores as a function of a modified Dukhin number: the case of 1:1 electrolytes	8
Computational and molecular dynamics simulation approach to analyze the impactof XPD gene mutation on protein stability and function	8
Brefeldin A variant via combinatorial screening acts as an effective antagonist inducing structural modification in EPAC2	8
Avoiding non-equilibrium effects in adaptive biasing force calculations	8
A DFT study on the adsorption of SO2 on Alx-C2N (x = 1, 2) monolayer	8
A review of recent advances in computational and experimental analysis of first adsorbed water layer on solid substrate	8
A simulation on the graphyne and its inorganic BN-like nanosheets as anode materials for Ca-ion batteries	8
Dehydration of acetic acid using layered graphene oxide (GO) membrane through forward osmosis (FO) process: a molecular dynamics study	7
Flat-histogram extrapolation as a useful tool in the age of big data	7
Estimation of diffusivity and intermolecular interaction strength of secondary and tertiary amine for CO2 absorption process by molecular dynamic simulation	7
Lithium and sodium ion binding in nanostructured carbon composites	7
Diffusion and reinforcement mechanism study of the effect of styrene/butadiene ratio on the high-temperature property of asphalt using molecular dynamics simulation	7
Unsupervised machine learning methods for polymer nanocomposites data via molecular dynamics simulation	7
Mechanism of urea decomposition catalyzed by Sporosarcina pasteurii urease based on quantum chemical calculations	7
Effects of poly-sulfide regenerant on the rejuvenated performance of SBS modified asphalt-binder	7
Dual targeting inhibitors for HIV-1 capsid and cyclophilin A: molecular docking, molecular dynamics, and quantum mechanics	7

Molecular dynamics simulation on structure evolution of silica glass in nano-cutting at high temperature	7
RUPTURA: simulation code for breakthrough, ideal adsorption solution theory computations, and fitting of isotherm models	7
Multi-scale evaluation of the mechanical properties of asphalt mortar under different aging conditions	7
Thermo-mechanical properties of different structures of BC2N	7
Structure-based virtual screening, ADMET profiling, and molecular dynamics simulation studies on HIV-1 protease for identification of active phytocompounds as potential anti-HIV agents	7
Free energy profiles of adsorption of surfactant micelles at metal-water interfaces	7
How to calculate pH-dependent binding rates for receptor–ligand systems based on thermodynamic simulations with different binding motifs	7
Modelling natural dye molecules lawsone and purpurin in different solvents for DSSC applications: a DFT and TD-DFT study	7
Predicting the efficiency of polyethylene glycol-functionalised graphene in delivery of temozolomide anticancer drug and investigating the effect of pH on the drug release process: DFT and free energy	7
Molecular simulation and experimental analysis on co-aging behaviors of SBS modifier and asphalt in SBS-modified asphalt	7
Thermal conductivity of perfect and defective carbon nanotubes functionalized with carbene: a molecular dynamics study	6
Effect of oxygen-containing functional groups of layered graphene oxide membrane on the removal of amoxicillin: a molecular dynamics study	6
Reproducibility of atomistic friction computer experiments: a molecular dynamics simulation study	6
Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments	6
Tensile properties of hydrogenated hybrid graphene–hexagonal boron nitride nanosheets: a reactive force field study	6
Inverse design of compression-induced solid – solid transitions in colloids	6
Static isotropic pressure induced ultra-wide band gap response of NaCaF3 fluoro-perovskite and its repercussions on optical properties: ab initio calculation	6
Computational study of nanoscale mechanical properties of Fe–Cr–Ni alloy	6
In-silico analysis of deleterious single nucleotide polymorphisms of PNMT gene	6
Motion of a tumour cell under the blood flow at low Reynolds number in a curved microvessel	6
A combined molecular docking and molecular dynamics simulation approach to probing the host–guest interactions of Ataluren with natural and modified cyclodextrins	6
Molecular dynamics simulations of nanoindentation – the importance of force field choice on the predicted elastic modulus of FCC aluminum	6
Implication of Ab Initio, QM/MM, and molecular dynamics calculations on the prediction of the therapeutic potential of some selected HDAC inhibitors	6
In silico study of the interactions of Pilocarpus microphyllus imidazolic alkaloids with the main protease (Mpro) of SARS-CoV-2	6
Molecular interaction studies of thymol via molecular dynamic simulations and free energy calculations using multi-target approach against Aedes aegypti proteome to decipher its role as mosquit	6
Removal and transformation mechanisms of nitrogen and sulfur in petcoke supercritical water gasification via ReaxFF simulation	6
The impact of the thermostats on the non-equilibrium computer simulations of the interfacial thermal conductance	6
Detonation response mechanism of shocked LLM-105 using ReaxFF-lg and MSST	6
Investigation of the thermal conductivity of tetrabenzo[8]circulene (TB8C) by molecular dynamics simulation	6
First-principles calculations to investigate structural, electronics, optical and mechanical properties of LaRu2P2 compound for superconducting application	6
Molecular-weight dependence of simulated glass transition temperature for isolated poly(ethylene oxide) chain	6
Molecular insights on the influence of temperature and metal ions on the hydration of kaolinite (001) surface	6
Molecular simulation of thermoset curing: application to 3D printing materials	6
First principle study on the mechanical response of ZrC and ZrN at high-pressure conditions: anisotropy perspective	6
Assessment of sulfobutylether-beta-cyclodextrin as a promising Fluorometholone molecule container: DFT, Docking, Molecular dynamics and MM-PBSA free energy calculations	6
Monte Carlo simulation and theoretical calculation of the thermodynamic properties of binary hard-core Lennard-Jones fluid mixtures	6
Rheological behaviour of shear thickening fluid of graphene oxide and SiO2 polyethylene glycol 400-based fluid with molecular dynamic simulation	6
Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer	6
The interface characteristics of TiN(100)/MgO(100) multilayer on oxidized Si(100) substrate via first-principle calculations and experimental investigation	6
Transformation mechanism of carbamic acid elimination and hydrolysis reaction in microbial self-healing concrete	5
Molecular modelling study on pyrrolo[2,3-b]pyridine derivatives as c-Met kinase inhibitors: a combined approach using molecular docking, 3D-QSAR modelling and molecular dynamics simulation	5
Effect of water medium on material removal and sub-surface defect evolution in nano-cutting of single-crystal γ-TiAl alloy	5
Micro-mechanical properties and damage mechanisms of coal under cyclic loading: A nanoindentation experiment and molecular dynamics simulation	5
Controversies about hydrogen bonds in water molecules on the influence of high magnetic fields: implications on structural and electronic parameters	5
Modified clustering algorithm for molecular simulation	5
Molecular dynamics simulations of performance degradation of cellulose nanofibers (CNFs) under hygrothermal environments	5
Simulating a heteroatomic CBN fullerene-like nanocage towards the drug delivery of fluorouracil	5
Virtual screening of potential inhibitor against breast cancer-causing estrogen receptor alpha (ERα): molecular docking and dynamic simulations	5
Local structure in lithium chloride solution: a Monte-Carlo simulation study	5
DFT study of gas adsorbing and electronic properties of unsaturated nanoporous graphene	5
Molecular insights into the corrosion inhibition mechanism of omeprazole and tinidazole: a theoretical investigation	5
Molecular dynamics simulation of nano-crack formation in asphalt binder with different SARA fractions	5
Anti-cancer potentials of aervine validated throughin silicomolecular docking, dynamics simulations, pharmacokinetic prediction andin vitroassessment of caspase – 3 in SW480 cell line	5
Molecular mechanism of thermal sensitization effect of potential materials for microwave hyperthermia	5
Combustion chemistry of n-heptane/ethanol blends: a ReaxFF study	5
In silico analysis: structural insights about inter-protofilaments interactions for α-synuclein (50–57) fibrils and its familial mutation	5
Computational study on the effect of steric hindrance in functionalised Zr-based metal-organic frameworks on hydrocarbon storage and separation	5
First-principles investigation of the structure and electronic properties of graphene toward Li adsorption	5
Modelling and structural investigation of a new DNA Origami based flexible bio-nano joint	5
Thermodynamic calculations using reverse Monte Carlo: convergence aspects, sources of error and guidelines for improving accuracy	5
Correlation between the fouling of different crystal calcium carbonate and Fe2O3 corrosion on heat exchanger surface	4
A first principles study of adsorption of hydrazine on C20, C40 and C60 fullerene nanoclusters	4
Effect of transverse dissipative particle dynamics on dynamic properties of nanometer-thick liquid films on solid surfaces	4
Decomposition mechanism of HCOOH on Pt/WC(0001) surfaces: a density functional theory study	4
Structural based investigation of novel pyrazole-thiazole Hybrids as dual CDK-1 and CDK-2 inhibitors for cancer chemotherapy	4
Microsolvation of phenol in water: structures, hydration free energy and enthalpy	4
Identifying and estimating bias in overlap-sampling free-energy calculations	4
Evaluation of CO2 absorption and stripping process for primary and secondary amines	4
Ionic liquid-air interface probed by sum frequency generation spectroscopy and molecular dynamics simulation: influence of alkyl chain length and anion volume	4
Detection of NOx and COx (x = 1, 2) molecules with T4,4,4-graphyne: a density functional theory study	4
Coherency spectral analysis of interfacial water at TiO2 surfaces	4
Hole transport nature exploration of 4,4-Difluoro-8-(C4H3X)-4-bora-3a,4a-diaza-s-indacene (X = O, S, Se) (BODIPY) systems	4
Conformational fingerprints in the modelling performance of MIA-QSAR: a case for SARS-CoV protease inhibitors	4
Molecular dynamics and intrinsic disorder analysis of the SARS-CoV-2 Nsp1 structural changes caused by substitution and deletion mutations	4
Molecular dynamics simulation and experimental study on mechanical properties and microstructure of cement-based composites enhanced by graphene oxide and graphene	4
Considerations when calculating the mechanical properties of single crystals and bulk polycrystals from molecular dynamics simulations	4
Conformational and intermolecular structure of stereoregular isomers of poly(acrylic acid) (PAA) and Na+-poly(acrylate) polyelectrolyte (Na+-PAA) in dilute aqueous solution: a mo	4
Solubility analysis of nano particles, cellulose crystalline region and cellulose molecule, and the impact study of crystalline region on properties of cellulose insulating paper	4
Molecular dynamics simulations reveal the mechanism of the interactions between the inhibitors and SIRT2 at atom level	4
Where is the hydrodynamic limit?	4

Improving thermodynamic properties and desorption temperature in MgH2 by doping Be: DFT study	4
Hydration inhibition mechanism of gypsum on tricalcium aluminate from ReaxFF molecular dynamics simulation and quantum chemical calculation	4
Molecular dynamics simulations of polymerisation and crystallisation at constant chemical potential	4
Atomistic approach to analyse transportation of water nanodroplet through a vibrating nanochannel: scope in bio-NEMS applications	4
Structural dynamics of Rhipicephalus microplus serpin-3	4
DFT simulation of barrier heights, infrared and Raman spectra, and investigation of vibrational characteristics of 2-((2-aminopyridin-3-yl) methylene) hydrazinecarbothioamide and its N-methyl v	4
Voltage–current behavior of 4-phenylamino-3-penten-2-one and its derivatives molecular switch: a first-principles study	4
Molecular dynamics perspective of condensation over a hybrid wetting surface	4
Aging resistance of polyurethane/graphene oxide composite modified asphalt: performance evaluation and molecular dynamics simulation	4
On the distance between A and B in molecular configuration space	4
Molecular dynamics simulation of the interfacial properties of methane-water and methane-brine systems	4
On the synergistic effect of asphaltene and surfactant to reduce n-dodecane–water interfacial tension: insights from molecular dynamics simulations	4
The metric resolvability and topological characterisation of some molecules in H1N1 antiviral drugs	4
A ReaxFF molecular dynamics study on the hydropyrolysis process of Huadian oil shale kerogen	4
Adsorption of organic compounds at the surface of Enceladus’ ice grains. A grand canonical Monte Carlo simulation study	4
First-principles characterisation and comparison of clean, hydrated, and defect α-Al2O3 and α-Fe2O3 (110) surfaces	4
Investigating the binding affinities of fructose and galactose to human serum albumin: simulation studies	4
Tensile deformation behaviours of polycrystalline Cu80Ni20 alloy: insights from molecular dynamics simulations	4
Mechanical properties of MoS2 nanotubes under tension: a molecular dynamics study	4
Optical properties enhancement of buckled Bismuthene in mid-infrared region: a theoretical first-principle study	4