Molecular Simulation

Article	Citations
A review of advancements in coarse-grained molecular dynamics simulations	108
Finite-size effects of diffusion coefficients computed from molecular dynamics: a review of what we have learned so far	90
COMPASS III: automated fitting workflows and extension to ionic liquids	88
RETRACTED ARTICLE: Ir-decorated gallium nitride nanotubes as a chemical sensor for recognition of mesalamine drug: a DFT study	64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	51
Recent advances in the continuous fractional component Monte Carlo methodology	40
Materials Studio 20th anniversary	37
The adsorption of chlorofluoromethane on pristine and Ge-doped silicon carbide nanotube: a PBC-DFT, NBO, and QTAIM study	35
Machine learning and descriptor selection for the computational discovery of metal-organic frameworks	30
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
Molecular modelling framework of metal-organic clusters for conserving surfaces: Langmuir sorption through the TD-DFT/ONIOM approach	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
Fast transport of water in carbon nanotubes: a review of current accomplishments and challenges	18
Reactive molecular dynamics simulation on the structure characteristics and tensile properties of calcium silicate hydrate at various temperatures and strain rates	17
Dimethyl and ethyl methyl ether adsorption studies on β-antimonene nanosheets – a first-principles study	17
Thermal conductivity and mechanical properties of graphene-like BC2, BC3 and B4C3	17
PoreMS: a software tool for generating silica pore models with user-defined surface functionalisation and pore dimensions	17
Novel green phosphorene as a superior gas sensor for dissolved gas analysis in oil transformers: using DFT method	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
A synergic effect of CNT/Al2O3 reinforcements on multiscale epoxy-based glass fiber composite: fabrication and molecular dynamics modeling	16

Study of the adsorption of chloropicrin on pure and Ga and Al doped B12N12: a comprehensive DFT and QTAIM investigation	16
Adaptive steered molecular dynamics of biomolecules	16
Molecular simulations of interfacial systems: challenges, applications and future perspectives	16
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	15
Acetaminophen and mepirizole molecular adsorption studies on novel ζ – phosphorene nanotube based on first-principles investigation	14
In silico toxicity investigation of Methaqualone’s conjunctival, retinal, and gastrointestinal hemorrhage by molecular modelling approach	14
Structural and vibrational spectral investigation on the identification of Non-Linear Optical properties and wave function analyses (electrostatic potential, electron localisation function, localised	14
Compatibility and high temperature performance of recycled polyethylene modified asphalt using molecular simulations	13
Molecular modelling of antiproliferative inhibitors based on SMILES descriptors using Monte-Carlo method, docking, MD simulations and ADME/Tox studies	13
A study of the microscopic interaction mechanism of styrene–butadiene-styrene modified asphalt based on density functional theory	13
Theoretical insights about inhibition efficiencies of some 8-Hydroxyqionoline derivatives against the corrosion of mild steel	12
A modified many-body dissipative particle dynamics model for mesoscopic fluid simulation: methodology, calibration, and application for hydrocarbon and water	12
Index of ideality of correlation and correlation contradiction index: a confluent perusal on acetylcholinesterase inhibitors	11
Theoretical studies of Thiazolyl-Pyrazoline derivatives as promising drugs against malaria by QSAR modelling combined with molecular docking and molecular dynamics simulation	11
RUPTURA: simulation code for breakthrough, ideal adsorption solution theory computations, and fitting of isotherm models	11
An in silico molecular dynamics simulation study on the inhibitors of SARS-CoV-2 proteases (3CLpro and PLpro) to combat COVID-19	11
Potential antifungal activity of novel carbohydrate derivatives validated by POM, molecular docking and molecular dynamic simulations analyses	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
Estimation of improvement in elastic moduli for functionalised defective graphene-based thermoplastic polyurethane nanocomposites: a molecular dynamics approach	10
Effects of poly-sulfide regenerant on the rejuvenated performance of SBS modified asphalt-binder	10
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	10
Temperature and its control in molecular dynamics simulations	10
Estimation of diffusivity and intermolecular interaction strength of secondary and tertiary amine for CO2 absorption process by molecular dynamic simulation	10
Effect of annealing temperature on photoluminescence spectra, gap states using different models and optical dispersion parameters in copper-doped ZnO films	9
Computational screening of metal–organic framework structures for separation of propane/propene mixture	9
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
Synthesis of 5, 6-diaroylisoindoline-1, 3-dione and computational approaches for investigation on structural and mechanistic insights by DFT	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
Coadsorption of Na+ and H2O on the surface of hydroxylated silica	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
Mechanism of urea decomposition catalyzed by Sporosarcina pasteurii urease based on quantum chemical calculations	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
A simulation on the graphyne and its inorganic BN-like nanosheets as anode materials for Ca-ion batteries	8
Modelling natural dye molecules lawsone and purpurin in different solvents for DSSC applications: a DFT and TD-DFT study	8
Avoiding non-equilibrium effects in adaptive biasing force calculations	8
Effects of Ag-decoration on the adsorption and detection of toxic OF2 gas on a GaN nanotube	8
Structural geometry, electronic structure, thermo-electronic and optical properties of GaCuO2 and GaCu0.94Fe0.06O2: a first principle approach of three DFT	8
A review of recent advances in computational and experimental analysis of first adsorbed water layer on solid substrate	8
Diffusion and reinforcement mechanism study of the effect of styrene/butadiene ratio on the high-temperature property of asphalt using molecular dynamics simulation	8
Computational binding study with α7 nicotinic acetylcholine receptor of Anvylic-3288: an allosteric modulator	8
A DFT study on the adsorption of SO2 on Alx-C2N (x = 1, 2) monolayer	8
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	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
Dual targeting inhibitors for HIV-1 capsid and cyclophilin A: molecular docking, molecular dynamics, and quantum mechanics	7

How to calculate pH-dependent binding rates for receptor–ligand systems based on thermodynamic simulations with different binding motifs	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
Static isotropic pressure induced ultra-wide band gap response of NaCaF3 fluoro-perovskite and its repercussions on optical properties: ab initio calculation	7
Dehydration of acetic acid using layered graphene oxide (GO) membrane through forward osmosis (FO) process: a molecular dynamics study	7
Molecular insights into the corrosion inhibition mechanism of omeprazole and tinidazole: a theoretical investigation	7
Molecular dynamics simulation on structure evolution of silica glass in nano-cutting at high temperature	7
Unsupervised machine learning methods for polymer nanocomposites data via molecular dynamics simulation	7
Molecular simulation and experimental analysis on co-aging behaviors of SBS modifier and asphalt in SBS-modified asphalt	7
A combined molecular docking and molecular dynamics simulation approach to probing the host–guest interactions of Ataluren with natural and modified cyclodextrins	7
Free energy profiles of adsorption of surfactant micelles at metal-water interfaces	7
Lithium and sodium ion binding in nanostructured carbon composites	7
Implication of Ab Initio, QM/MM, and molecular dynamics calculations on the prediction of the therapeutic potential of some selected HDAC inhibitors	6
Evaluation of CO2 absorption and stripping process for primary and secondary amines	6
First principle study on the mechanical response of ZrC and ZrN at high-pressure conditions: anisotropy perspective	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
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
The interface characteristics of TiN(100)/MgO(100) multilayer on oxidized Si(100) substrate via first-principle calculations and experimental investigation	6
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
Molecular simulation of thermoset curing: application to 3D printing materials	6
First-principles investigation of the structure and electronic properties of graphene toward Li adsorption	6
Computational study of nanoscale mechanical properties of Fe–Cr–Ni alloy	6
Tensile properties of hydrogenated hybrid graphene–hexagonal boron nitride nanosheets: a reactive force field study	6
Rheological behaviour of shear thickening fluid of graphene oxide and SiO2 polyethylene glycol 400-based fluid with molecular dynamic simulation	6
Transformation mechanism of carbamic acid elimination and hydrolysis reaction in microbial self-healing concrete	6
In-silico analysis of deleterious single nucleotide polymorphisms of PNMT gene	6
Investigation of the thermal conductivity of tetrabenzo[8]circulene (TB8C) by molecular dynamics simulation	6
Motion of a tumour cell under the blood flow at low Reynolds number in a curved microvessel	6
Molecular dynamics simulations of nanoindentation – the importance of force field choice on the predicted elastic modulus of FCC aluminum	6
Molecular insights on the influence of temperature and metal ions on the hydration of kaolinite (001) surface	6
Mathematical and computational models of RNA nanoclusters and their applications in data-driven environments	6
Thermodynamic calculations using reverse Monte Carlo: convergence aspects, sources of error and guidelines for improving accuracy	6
In silico study of the interactions of Pilocarpus microphyllus imidazolic alkaloids with the main protease (Mpro) of SARS-CoV-2	6
Molecular dynamics simulation of nano-crack formation in asphalt binder with different SARA fractions	6
Detonation response mechanism of shocked LLM-105 using ReaxFF-lg and MSST	6
Virtual screening of potential inhibitor against breast cancer-causing estrogen receptor alpha (ERα): molecular docking and dynamic simulations	6
Removal and transformation mechanisms of nitrogen and sulfur in petcoke supercritical water gasification via ReaxFF simulation	6
Inverse design of compression-induced solid – solid transitions in colloids	6
The impact of the thermostats on the non-equilibrium computer simulations of the interfacial thermal conductance	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
Reproducibility of atomistic friction computer experiments: a molecular dynamics simulation study	6
Effect of water medium on material removal and sub-surface defect evolution in nano-cutting of single-crystal γ-TiAl alloy	5
Computational study on the effect of steric hindrance in functionalised Zr-based metal-organic frameworks on hydrocarbon storage and separation	5
Modelling and structural investigation of a new DNA Origami based flexible bio-nano joint	5
Anti-cancer potentials of aervine validated throughin silicomolecular docking, dynamics simulations, pharmacokinetic prediction andin vitroassessment of caspase – 3 in SW480 cell line	5
Simulating a heteroatomic CBN fullerene-like nanocage towards the drug delivery of fluorouracil	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
In silico analysis: structural insights about inter-protofilaments interactions for α-synuclein (50–57) fibrils and its familial mutation	5
DFT study of gas adsorbing and electronic properties of unsaturated nanoporous graphene	5
Micro-mechanical properties and damage mechanisms of coal under cyclic loading: A nanoindentation experiment and molecular dynamics simulation	5
Atomistic approach to analyse transportation of water nanodroplet through a vibrating nanochannel: scope in bio-NEMS applications	5
Molecular dynamics simulations of performance degradation of cellulose nanofibers (CNFs) under hygrothermal environments	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
A first principles study of adsorption of hydrazine on C20, C40 and C60 fullerene nanoclusters	5
Molecular insight into the structure and dynamics of LiTf2N/deep eutectic solvent: an electrolyte for Li-ion batteries	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
Effects of chain length on the structure and dynamics of polyvinyl chloride during atomistic molecular dynamics simulations	5
Local structure in lithium chloride solution: a Monte-Carlo simulation study	5
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
Aging resistance of polyurethane/graphene oxide composite modified asphalt: performance evaluation and molecular dynamics simulation	4
Decomposition mechanism of HCOOH on Pt/WC(0001) surfaces: a density functional theory study	4
Improving thermodynamic properties and desorption temperature in MgH2 by doping Be: DFT study	4
On the synergistic effect of asphaltene and surfactant to reduce n-dodecane–water interfacial tension: insights from molecular dynamics simulations	4
Ionic liquid-air interface probed by sum frequency generation spectroscopy and molecular dynamics simulation: influence of alkyl chain length and anion volume	4
Identifying and estimating bias in overlap-sampling free-energy calculations	4
Tensile deformation behaviours of polycrystalline Cu80Ni20 alloy: insights from molecular dynamics simulations	4
Investigating the binding affinities of fructose and galactose to human serum albumin: simulation studies	4
First-principles characterisation and comparison of clean, hydrated, and defect α-Al2O3 and α-Fe2O3 (110) surfaces	4
Mechanical properties of MoS2 nanotubes under tension: a molecular dynamics study	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
Molecular dynamics perspective of condensation over a hybrid wetting surface	4
Molecular dynamics and intrinsic disorder analysis of the SARS-CoV-2 Nsp1 structural changes caused by substitution and deletion mutations	4
Molecular dynamics simulations of friction behaviours on nano-textured silicon surfaces	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
Structural based investigation of novel pyrazole-thiazole Hybrids as dual CDK-1 and CDK-2 inhibitors for cancer chemotherapy	4
Novel inhibitors design through structural investigations and simulation studies for human PKMTs (SMYD2) involved in cancer	4

Adsorption of organic compounds at the surface of Enceladus’ ice grains. A grand canonical Monte Carlo simulation study	4
Microsolvation of phenol in water: structures, hydration free energy and enthalpy	4
Where is the hydrodynamic limit?	4
Nucleation and relaxation processes in weak solutions: molecular dynamics simulation	4
Coherency spectral analysis of interfacial water at TiO2 surfaces	4
Detection of NOx and COx (x = 1, 2) molecules with T4,4,4-graphyne: a density functional theory study	4
Conformational fingerprints in the modelling performance of MIA-QSAR: a case for SARS-CoV protease inhibitors	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
Orientation-dependent electrostatic interaction between inverse patchy colloids	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
Effect of transverse dissipative particle dynamics on dynamic properties of nanometer-thick liquid films on solid surfaces	4
Application of T4,4,4-graphyne for anode of Na-ion battery: first principle theoretical study	4
Molecular dynamics simulations of polymerisation and crystallisation at constant chemical potential	4
The metric resolvability and topological characterisation of some molecules in H1N1 antiviral drugs	4
Porous material adsorbents ZIF-8, ZIF-67, Co/Zn-ZIF and MIL-127(Fe) for separation of H 2 S from a H 2 S/CH 4	4
First-principles calculations to investigate structural, mechanical, electronic, optical, and thermoelectric properties of novel cubic double Perovskites X2AgBiBr6 (X=Li, Na, K, Rb, Cs) for optoelectr	4
Hydration inhibition mechanism of gypsum on tricalcium aluminate from ReaxFF molecular dynamics simulation and quantum chemical calculation	4
Structural dynamics of Rhipicephalus microplus serpin-3	4
A ReaxFF molecular dynamics study on the hydropyrolysis process of Huadian oil shale kerogen	4
Correlation between the fouling of different crystal calcium carbonate and Fe2O3 corrosion on heat exchanger surface	4
Optical properties enhancement of buckled Bismuthene in mid-infrared region: a theoretical first-principle study	4
First-principles calculations to investigate optical and electrical properties of the half-Heusler materials TiXSn (X = Ni, Pt)	4
Molecular dynamics simulation of the interfacial properties of methane-water and methane-brine systems	4