Impact of pathogenic mutations of the GLUT1 glucose transporter on solute carrier dynamics using ComDYN enhanced sampling [version 2; peer review: 2 approved, 1 approved with reser... by K. Anton Feenstra, Akiko Higuchi, Kei Yura, Sanne Abeln, Halima Mouhib

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Research Progress on Nano-Confinement Effects in Unconventional Oil and Gas Energy—With a Major Focus on Shale Reservoirs by Guo Wang, Rui Shen, Shengchun Xiong, Yuhao Mei, Qinghao Dong, Shasha Chu, Heying Su, Xuewei Liu

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Drug Target Investigation of <i>N</i>-<i>p</i>-Coumaroyl-<i>N</i>’-Caffeoylputrescine, a Naturally-Occurring Alkaloid Derived from <i>Saxifraga tangutica</i> by Chuang Liu, Jun Dang, Minchen Wu

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Correlation analysis between micro and macro indicators of high modulus modified asphalt for asphalt pavement. by Jiarong Wang, Zhengqi Zhang, Zhongnan Tian

“…Secondly, Molecular models of two kinds of HMA were established through molecular dynamics (MD) simulations, and the high temperature parameters of LLDPE/SBS composite modified asphalt were obtained with the two methods, namely the micro molecular dynamics simulation and high temperature rheological test, respectively. …”
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Distinct creep regimes of methane hydrates predicted by a monatomic water model by Henrik Andersen Sveinsson, Pinqiang Cao

“…Here we show, using molecular dynamics simulations spanning almost 2 orders of magnitude of stresses and 3 orders of magnitude of strain rates, that such power-law creep emerges in molecular dynamics simulations of polycrystalline methane hydrates using a monatomic water model, suggesting that only simplified molecular interactions and the concept of a hydrate polycrystal are needed for such power-law creep behavior to emerge. …”
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Anomalous entropy-driven kinetics of dislocation nucleation by Soumendu Bagchi, Danny Perez

“…These observations suggest possible explanations to previously observed unconventional deformation kinetics in both molecular dynamics simulations and experiments.…”
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THE NUMERICAL SIMULATIONSTUDY SPANNING THE CONTINUUM/ATOMS SCALEON THE TYPE Ⅰ EDGE CRACK PROPAGATION PROCESS IN SINGLE CRYSTAL SILVERBASED ON THEDISPLACEMENT CONNECTION by SONG Kun, WANG LuSheng, LIU Bo, DING Jun, HUANG Xia, HE XiaoJin

“…The finite element method（ FEM） and molecular dynamics simulation（ MD） were combined to simulate the multi-scale models,and the stress intensity factors（ SIF） and displacement mechanics parameters were adopted to connect and convertthecontinuum region and discrete molecular dynamics region,then three multi-scale model of two-dimensional silver crack propagationwasestablished to obtain the crack tip trajectory and the micro-scale crackpropagationprocess. …”
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Advancements in surface-enhanced femtosecond stimulated Raman spectroscopy: exploring factors influencing detectability and shapes of spectra by Pyrcz Patryk, Gawinkowski Sylwester

“…A combination of femtosecond stimulated Raman scattering and surface-enhanced Raman scattering, termed surface-enhanced stimulated Raman scattering (SE-FSRS), was proposed to leverage both temporal precision and sensitivity for advanced molecular dynamics analysis. During the initial successful implementations of this approach, unexpected spectral distortions were observed, and several potential explanations were proposed. …”
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Thiazolo-pyridopyrimidines: An in silico evaluation as a lead for CDK4/6 inhibition, synthesis and cytotoxicity screening against breast cancer cell lines by Chaithra R Shetty, C. S. Shastry, Parasuraman P, Srinivas Hebbar

“…To further evaluate stability, molecular dynamics simulations were conducted for the two most promising compounds within the binding site. …”
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Unveiling molecular insights: in silico exploration of TLR4 antagonist for management of dry eye syndrome by Kothandan Sudhakar, Neeru Dugar, Srikanth Jupudi, Ravichandran Ashwin, Kuppusamy Gowthamarajan

“…Among the three compounds, celastrol was the most stable based on molecular dynamics trajectory analysis from 100 ns in the catalytic pockets of 2Z63.pdb.pdb. …”
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INVESTIGATING CHOLAGOGUE AND CHOLERETIC ACTIVITY OF PEUMUS BOLDUS by Raphael S. F. Silva, Marcus Vinícius H. Faria, Joyce F. S. D. de Almeida, Tanos C. C. França

“…The packages MOPAC, AutoDock, GROMACS and g_mmpbsa were employed for structural optimization, molecular docking, molecular dynamics and bond energy calculations respectively. …”
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Computational Modeling of the Interaction of Silver Nanoparticles with the Lipid Layer of the Skin by Andrea Fabara, Sebastián Cuesta, Fernanda Pilaquinga, Lorena Meneses

“…Silver nanoparticles seemed to have very good clearance properties in our molecular dynamics simulation because over a certain period of time, the silver cluster got far away from the biological molecules.…”
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Potential Azo-8-hydroxyquinoline derivatives as multi-target lead candidates for Alzheimer's disease: An in-depth in silico study of monoamine oxidase and cholinesterase inhibitors... by Fatima Zahra Guerguer, Bouchra Rossafi, Oussama Abchir, Yasir S Raouf, Dhabya Bakhit Albalushi, Abdelouahid Samadi, Samir Chtita

“…An exhaustive in silico analysis was conducted, encompassing docking studies, ADMET analysis, density functional theory (DFT) studies, molecular dynamics simulations, and subsequent MM-GBSA calculations to examine the pharmacological potential of these molecules with the specific targets of interest. …”
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Unbinding of alpha chain of hemoglobin in sickle and normal structures by Jhulan Powrel, Rajendra Prasad Koirala, Narayan Prasad Adhikari

“…The estimated parameters from sickle hemoglobin is compared to normal hemoglobin structure. Steered Molecular Dynamics (SMD) has been utilized to estimate the force required in breaking hydrogen bonds in given chains. …”
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Alpiniae oxyphyllae Fructus ameliorates renal lipid accumulation in diabetic kidney disease via activating PPARα by Zi-Jie Yan, Lin Zhang, Xin-Yao Han, Yu Kang, Shu-Man Liu, Tian-Peng Ma, Man Xiao, Yi-Qiang Xie

“…Results: Network pharmacological enrichment analysis, molecular docking, and molecular dynamics simulation showed that the active compounds in AOF targeted PPARα and thus transcriptionally regulated ACOX1 and CPT1A. …”
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An In Silico Study of the Interactions of Alkaloids from Cryptolepis sanguinolenta with Plasmodium falciparum Dihydrofolate Reductase and Dihydroorotate Dehydrogenase by Lois Kwane Kyei, Edward Ntim Gasu, Gilbert Boadu Ampomah, Jehoshaphat Oppong Mensah, Lawrence Sheringham Borquaye

“…Therefore, molecular docking and molecular dynamics simulations were used to investigate the interactions and stability of the alkaloids with PfDHFR and PfDHODH. …”
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Double resonance spectroscopy reveals structure and dynamics near transition states by Joshua H. Baraban, Robert W. Field

“…A shared ambition of molecular spectroscopy and molecular dynamics is to establish the truths of chemical intuition on solid physical bedrock. …”
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Molecular origin of asymmetric yield surface of crosslinked epoxy polymers by Jinyoung Kim, Kyeongmin Hong, Yong-Seok Choi, Dayoung Jang, Jang-Woo Han, Hyungbum Park

“…In this study, we investigate the multiaxial mechanical behavior of thermosetting epoxy polymers and explore the asymmetry between tension and compression in their yield surfaces at the molecular level using molecular dynamics simulations, complemented by experimental validation through polymer synthesis. …”
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Interaction of α-Cembrenediol with Human Serum Albumin Based on Spectroscopic and Computational Analyses by Xian-Kun Su, Zhen-Chun Sun, Chang-You Zhao, Hui Yang, Tian-Ming Zhao, Chao Ma, Guo-Fei Zhu

“…To this end, we utilized various methods including UV absorption spectroscopy, steady-state fluorescence analysis, circular dichroism measurements, molecular docking studies, and molecular dynamics simulations. The results of the UV and fluorescence spectra clearly demonstrated that HSA interacts with α-cembrenediol. …”
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Virtual Screening, Toxicity Evaluation and Pharmacokinetics of Erythrina Alkaloids as Acetylcholinesterase Inhibitor Candidates from Natural Products by Permana A, Akili AWR, Hardianto A, Latip JB, Sulaeman AP, Herlina T

“…The top alkaloid, 8-oxoerymelanthine ( 128), was subjected to further analysis through molecular dynamics simulations, with the objective of evaluating its stability and interactions. …”
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