Evaluating the uncertainty in mean residual times: estimators based on residence times from discrete time processes. (English) Zbl 1543.62567
MSC:
62N05
Found 125 Documents (Results 1–100)
SPIRAL: an efficient algorithm for the integration of the equation of rotational motion. (English) Zbl 07826294
Unraveling the complexity of Exendin-4 folding through two distinct pathways. (English) Zbl 1531.92034
Random batch sum-of-Gaussians method for molecular dynamics simulations of particle systems. (English) Zbl 07749373
GPU-based molecular dynamics of turbulent liquid flows with OpenMM. (English) Zbl 1533.65009
Wyrzykowski, Roman (ed.) et al., Parallel processing and applied mathematics. 14th international conference, PPAM 2022, Gdansk, Poland, September 11–14, 2022. Revised selected papers. Part I. Cham: Springer. Lect. Notes Comput. Sci. 13826, 346-358 (2023).
Breaking down the parallel performance of GROMACS, a high-performance molecular dynamics software. (English) Zbl 1533.65008
Wyrzykowski, Roman (ed.) et al., Parallel processing and applied mathematics. 14th international conference, PPAM 2022, Gdansk, Poland, September 11–14, 2022. Revised selected papers. Part I. Cham: Springer. Lect. Notes Comput. Sci. 13826, 333-345 (2023).
How accurate does Newton have to be? (English) Zbl 1533.65074
Wyrzykowski, Roman (ed.) et al., Parallel processing and applied mathematics. 14th international conference, PPAM 2022, Gdansk, Poland, September 11–14, 2022. Revised selected papers. Part I. Cham: Springer. Lect. Notes Comput. Sci. 13826, 3-15 (2023).
A critical review on molecular dynamics applied to structure fracture and failure analysis. (English) Zbl 1511.74016
Multiscale hybrid modeling of proteins in solvent: SARS-CoV2 spike protein as test case for lattice Boltzmann – all atom molecular dynamics coupling. (English) Zbl 1508.92084
Computing committors in collective variables via Mahalanobis diffusion maps. (English) Zbl 1528.65007
N ways to simulate short-range particle systems: automated algorithm selection with the node-level library AutoPas. (English) Zbl 07699243
MSC:
68-XX
LAMMPS – a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. (English) Zbl 1516.74108
The effective hydrodynamic radius in the Stokes-Einstein relation is not a constant. (English) Zbl 1511.76077
A scalable algorithm for many-body dissipative particle dynamics using multiple general purpose graphic processing units. (English) Zbl 07682147
Connecting the dots: numerical randomized Hamiltonian Monte Carlo with state-dependent event rates. (English) Zbl 07633317
MSC:
62-XX
High-performance large-scale atomistic simulation of thin films deposition. (English) Zbl 1502.82024
Physics-informed distribution transformers via molecular dynamics and deep neural networks. (English) Zbl 07578917
Spectral gap of replica exchange Langevin diffusion on mixture distributions. (English) Zbl 1492.60218
A hybrid lattice Boltzmann-molecular dynamics-immersed boundary method model for the simulation of composite foams. (English) Zbl 1490.76166
Length scale effect on the buckling behavior of a graphene sheets using modified couple stress theory and molecular dynamics method. (English) Zbl 1492.74042
GROMACS implementation of free energy calculations with non-pairwise variationally derived intermediates. (English) Zbl 1539.82409
Molecular dynamics simulation of heat transfer and stresses in thin films caused by a short laser pulse. (English) Zbl 1479.82122
Dimensionality reduction of complex metastable systems via kernel embeddings of transition manifolds. (English) Zbl 1466.37068
Parallelization of a stochastic Euler-Lagrange model applied to large scale dense bubbly flows. (English) Zbl 07785537
A generalized Newton iteration for computing the solution of the inverse Henderson problem. (English) Zbl 1461.65109
Molecular dynamics simulations of the full-length prion protein. (English) Zbl 1453.92104
MSC:
92C40
Molecular dynamics performance evaluation with modern computer architecture. (English) Zbl 07250764
Sergeyev, Yaroslav D. (ed.) et al., Numerical computations: theory and algorithms. Third international conference, NUMTA 2019, Crotone, Italy, June 15–21, 2019. Revised selected papers. Part II. Cham: Springer. Lect. Notes Comput. Sci. 11974, 322-329 (2020).
MSC:
65-XX
The mechanism of pulsed electric field (PEF) targeting location on the spatial conformation of pine nut peptide. (English) Zbl 1464.92107
A data-driven framework for sparsity-enhanced surrogates with arbitrary mutually dependent randomness. (English) Zbl 1441.60004
Numerical aspect of large-scale electronic state calculation for flexible device material. (English) Zbl 1418.65048
Landmark diffusion maps (L-dMaps): accelerated manifold learning out-of-sample extension. (English) Zbl 1489.68228
Rational design, conformational analysis and membrane-penetrating dynamics study of Bac2A-derived antimicrobial peptides against gram-positive clinical strains isolated from pyemia. (English) Zbl 1414.92198
Generalized Fickian approach for phase separating fluid mixtures in smoothed particle hydrodynamics. (English) Zbl 1411.76135
Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson’s disease: A molecular dynamics simulation approach. (English) Zbl 1411.92229
MSC:
92D20
Insights into the interaction of key biofilm proteins in Pseudomonas aeruginosa PAO1 with TiO\(_2\) nanoparticle: an in silico analysis. (English) Zbl 1406.92168
In silico analysis of plasmodium falciparum CDPK5 protein through molecular modeling, docking and dynamics. (English) Zbl 1406.92209
Exploration of synthetic multifunctional amides as new therapeutic agents for Alzheimer’s disease through enzyme inhibition, chemoinformatic properties, molecular docking and dynamic simulation insights. (English) Zbl 1406.92303
An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates. (English) Zbl 1390.60190
Single channel quantum color image encryption algorithm based on HSI model and quantum Fourier transform. (English) Zbl 1387.81109
Molecular dynamics study of multicomponent droplet dissolution in a sparingly miscible liquid. (English) Zbl 1419.76637
MSC:
76T10
Task-based parallel computation of the density matrix in quantum-based molecular dynamics using graph partitioning. (English) Zbl 1383.82005
Reviewer: Vicenţiu D. Rădulescu (Craiova)
A novel method for calculating relative free energy of similar molecules in two environments. (English) Zbl 1376.80009
Numerical modelling of ion transport in 5-HT3 serotonin receptor using molecular dynamics. (English) Zbl 1394.65048
Dimov, Ivan (ed.) et al., Numerical analysis and its applications. 6th international conference, NAA 2016, Lozenetz, Bulgaria, June 15–22, 2016. Revised selected papers. Cham: Springer (ISBN 978-3-319-57098-3/pbk; 978-3-319-57099-0/ebook). Lecture Notes in Computer Science 10187, 195-202 (2017).
A comparative molecular dynamics-phase-field modeling approach to brittle fracture. (English) Zbl 1439.74369
Adaptive multi-stage integrators for optimal energy conservation in molecular simulations. (English) Zbl 1422.65447
Efficient implementation of the many-body reactive bond order (REBO) potential on GPU. (English) Zbl 1349.82031
A sparse Markov chain approximation of LQ-type stochastic control problems. (English) Zbl 1350.49031
Math. Control Relat. Fields 6, No. 3, 363-389 (2016); Addendum 7, No. 4, 623 (2017).
Petri nets formalism facilitates analysis of complex biomolecular structural data. (English) Zbl 1338.90078
Normal mode dynamics of voltage-gated \(\mathrm{K}^+\) channels: gating principle, opening mechanism, and inhibition. (English) Zbl 1409.92040
MSC:
92C20
Molecular crowding effects on conformation and stability of G-quadruplex DNA structure: insights from molecular dynamics simulation. (English) Zbl 1405.92222
\(\Pi\)4U: a high performance computing framework for Bayesian uncertainty quantification of complex models. (English) Zbl 1352.65009
A semi-analytical approach to molecular dynamics. (English) Zbl 1349.65206
MSC:
65L04
Wavelets as basis functions to represent the coarse-graining potential in multiscale coarse graining approach. (English) Zbl 1349.65736
MSC:
65T60
82C80
Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation. (English) Zbl 1314.92120
MSC:
92D20
Molecular dynamics. With deterministic and stochastic numerical methods. (English) Zbl 1351.82001
Interdisciplinary Applied Mathematics 39. Cham: Springer (ISBN 978-3-319-16374-1/hbk; 978-3-319-16375-8/ebook). xxii, 443 p. (2015).
Reviewer: Georg Hebermehl (Berlin)
Molecular modeling and molecular dynamics simulations of GPI 14 in Leishmania major: insight into the catalytic site for active site directed drug design. (English) Zbl 1412.92179
Molecular modeling, simulation and virtual screening of ribosomal phosphoprotein P1 from Plasmodium falciparum. (English) Zbl 1411.92099
Systematic detection of hidden complexities in the unfolding mechanism of a cytosine-rich DNA strand. (English) Zbl 1395.92114
Automated parameterization of intermolecular pair potentials using global optimization techniques. (English) Zbl 1360.65174
A stochastic thermostat algorithm for coarse-grained thermomechanical modeling of large-scale soft matters: theory and application to microfilaments. (English) Zbl 1349.74096
MSC:
74F05
Guided motion of short carbon nanotube driven by non-uniform electric field. (English) Zbl 1317.74074
ZIBgridfree: efficient conformational analysis by partition-of-unity coupling. (English) Zbl 1298.92123
Virtual model validation of complex multiscale systems: applications to nonlinear elastostatics. (English) Zbl 1286.62016
A meshless discretization method for Markov state models applied to explicit water peptide folding simulations. (English) Zbl 1269.82072
Griebel, Michael (ed.) et al., Meshfree methods for partial differential equations VI. Selected papers of the sixth international workshop, Bonn, Germany, October 4–6, 2011. Berlin: Springer (ISBN 978-3-642-32978-4/hbk; 978-3-642-32979-1/ebook). Lecture Notes in Computational Science and Engineering 89, 141-154 (2013).
ESPResSO 3.1: molecular dynamics software for coarse-grained models. (English) Zbl 1269.82007
Griebel, Michael (ed.) et al., Meshfree methods for partial differential equations VI. Selected papers of the sixth international workshop, Bonn, Germany, October 4–6, 2011. Berlin: Springer (ISBN 978-3-642-32978-4/hbk; 978-3-642-32979-1/ebook). Lecture Notes in Computational Science and Engineering 89, 1-23 (2013).
Combining stochastic and deterministic approaches within high efficiency molecular simulations. (English) Zbl 1264.82077
A modified amino acid network model contains similar and dissimilar weight. (English) Zbl 1261.92011
GANM: A protein-ligand docking approach based on genetic algorithm and normal modes. (English) Zbl 1284.92028
A coarse graining method for the dimension reduction of the state space of biomolecules. (English) Zbl 1309.92036
MSC:
92C40
Molecular dynamics simulation of HIV fusion inhibitor T-1249: insights on peptide-lipid interaction. (English) Zbl 1239.92032
A short note on the fast evaluation of dihedral angle potentials and their derivatives. (English) Zbl 1245.82002
MSC:
82-08
Orientations of special water dipoles that accelerate water molecules exiting from carbon nanotube. (English) Zbl 1238.81190
Fast analytical methods for macroscopic electrostatic models in biomolecular simulations. (English) Zbl 1228.92008
Implementing molecular dynamics on hybrid high performance computers-short range forces. (English) Zbl 1221.82008
Convergence analysis of truncated incomplete Hessian Newton minimization method and application in biomolecular potential energy minimization. (English) Zbl 1219.90189
A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization. (English) Zbl 1403.92219
MSC:
92D20
Protein interaction network analysis – approach for potential drug target identification in Mycobacterium tuberculosis. (English) Zbl 1403.92073
Bone remodelling in BioShape. (English) Zbl 1283.92010
Krivine, Jean (ed.) et al., Proceedings of the 1st international workshop on interactions between computer science and biology (CS2Bio’10), Amsterdam, The Netherlands, June 10, 2010. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 268, 17-29 (2010).
MSC:
92C05
Filter Results by …
Document Type
- Journal Articles (113)
- Collection Articles (10)
- Books (2)
all
top 5
Author
- Weber, Marcus (4)
- Akhmatskaya, Elena (3)
- Fackeldey, Konstantin (3)
- Xu, Zhenli (3)
- Aktulga, Hasan Metin (2)
- Alexov, Emil (2)
- Anderson, Joshua A. (2)
- Baker, Nathan A. (2)
- Bou-Rabee, Nawaf M. (2)
- Brown, W. Michael (2)
- Bujotzek, Alexander (2)
- Gao, Huajian (2)
- Gonnet, Pedro (2)
- Hartmann, Carsten (2)
- Hu, Guohui (2)
- Junghans, Christoph (2)
- Kong, Yong (2)
- Lei, Huan (2)
- Lulu, Sajitha (2)
- Plimpton, Steven J. (2)
- Sanz-Serna, Jesús María (2)
- Schütte, Christof (2)
- Shen, Zuowei (2)
- Shi, Xinghua (2)
- Sulimov, Vladimir B. (2)
- Tikhonravov, Alexander V. (2)
- Yang, Jianbin (2)
- Zhou, Zhewei (2)
- Abbasi, Muhammad Athar (1)
- Agrahari, Ashish Kumar (1)
- Ahmadi, Samrand Rash (1)
- An, Meiwen (1)
- Ananthasuresh, G. K. (1)
- Andersson, Måns I. (1)
- Andriukaitis, Darius (1)
- Angelidakis, Vasileios (1)
- Angelikopoulos, Panagiotis (1)
- Anishetty, Sharmila (1)
- Antonov, Mikhail Yu. (1)
- Anupama, Rani (1)
- Arnold, Axel (1)
- Ataei, Mohammadmehdi (1)
- Aziz-ur-Rehman (1)
- Babu, Subramanian (1)
- Bai, Xiaolu (1)
- Baltussen, M. W. (1)
- Banisch, Ralf (1)
- Barakos, George N. (1)
- Bauman, Paul T. (1)
- Bayazitoglu, Yildiz (1)
- Baz, Jörg (1)
- Berendsen, Herman J. C. (1)
- Berger, Richard (1)
- Bittracher, Andreas (1)
- Board, John A. jun. (1)
- Bolintineanu, Dan S. (1)
- Bonaccorso, Fabio (1)
- Bowers, Kevin J. (1)
- Bozorgmehr, Mohammad Reza (1)
- Braz, Antonio Sérgio Kimus (1)
- Breuza, Emanuele (1)
- Bu, Bing (1)
- Buist, K. A. (1)
- Bungartz, Hans-Joachim (1)
- Burstedde, Carsten (1)
- Bussmann, Markus (1)
- Buti, Federico (1)
- Cacciagrano, Diletta Romana (1)
- Cai, Difeng (1)
- Cai, Wei (1)
- Cameron, Maria Kourkina (1)
- Carvalho, A. J. Palace (1)
- Casoni, E. (1)
- Castagna, Jony (1)
- Chen, Kaixian (1)
- Chen, Weiyi (1)
- Chen, Xiaolin (1)
- Chesnokov, D. A. (1)
- Chiodo, Letizia (1)
- Clark, Tim W. (1)
- Colombo, Giorgio (1)
- Corradini, Flavio (1)
- Costa, Franco S. (1)
- Crozier, Paul S. (1)
- Cruz-Chú, Eduardo R. (1)
- Danani, Andrea (1)
- del Valle, Carlos Andrés (1)
- Delbary, Fabrice (1)
- Desbrun, Mathieu (1)
- Di Giusto, Davide (1)
- Diao, Jiajie (1)
- Dill, Ken A. (1)
- Dittmer, Evelyn (1)
- Djamal, Chaabane (1)
- Donati, Luca (1)
- Dong, Jing (1)
- Doss, George Priya C. (1)
- Dror, Ron O. (1)
- Durve, Mihir (1)
- Eguzkitza, Beatriz (1)
- and 322 more Authors
all
top 5
Serial
- J. Comput. Phys. (18)
- J. Theor. Biol. (13)
- Comput. Phys. Commun. (10)
- SIAM J. Sci. Comput. (5)
- Comput. Biol. Chem. (4)
- Comput. Methods Appl. Mech. Eng. (3)
- Appl. Math. Mech., Engl. Ed. (3)
- Appl. Comput. Harmon. Anal. (3)
- J. Math. Chem. (3)
- Lobachevskii J. Math. (3)
- Acta Mech. Sin. (3)
- Comput. Math. Methods Med. (3)
- J. Stat. Phys. (2)
- Commun. Comput. Phys. (2)
- Acta Mech. (1)
- Comput. Fluids (1)
- Comput. Math. Appl. (1)
- Int. J. Heat Mass Transfer (1)
- Int. J. Numer. Methods Fluids (1)
- Int. J. Theor. Phys. (1)
- J. Fluid Mech. (1)
- J. Mech. Phys. Solids (1)
- Math. Biosci. (1)
- Physica A (1)
- ACM Trans. Math. Softw. (1)
- Appl. Math. Comput. (1)
- Int. J. Numer. Methods Eng. (1)
- Comput. Mech. (1)
- Japan J. Ind. Appl. Math. (1)
- Numer. Algorithms (1)
- SIAM Rev. (1)
- Stochastic Processes Appl. (1)
- J. Nonlinear Sci. (1)
- Comput. Optim. Appl. (1)
- J. Comput. Neurosci. (1)
- Eng. Anal. Bound. Elem. (1)
- Int. Trans. Oper. Res. (1)
- Chaos (1)
- Proc. R. Soc. Lond., Ser. A, Math. Phys. Eng. Sci. (1)
- Commun. Nonlinear Sci. Numer. Simul. (1)
- RAIRO, Oper. Res. (1)
- Arch. Comput. Methods Eng. (1)
- Entropy (1)
- Cent. Eur. J. Math. (1)
- Int. J. Geom. Methods Mod. Phys. (1)
- Acta Numerica (1)
- Inverse Probl. Sci. Eng. (1)
- Interdiscip. Appl. Math. (1)
- Commun. Theor. Phys. (1)
- J. Comput. Graph. Stat. (1)
- Math. Control Relat. Fields (1)
- Mol. Based Math. Biol. (1)
- J. Comput. Phys.: X (1)
all
top 3
Software
- Gromacs (125)
- LINCS (18)
- CHARMM (16)
- NAMD (16)
- LAMMPS (10)
- VMD (10)
- AMBER (7)
- CUDA (7)
- PROCHECK (6)
- APBS (5)
- GROMOS (5)
- I-TASSER (5)
- FFTW (4)
- GSHMC (4)
- OpenMM (4)
- SETTLE (4)
- Chimera (3)
- DESMOND (3)
- DL_POLY (3)
- ESPResSo (3)
- GitHub (3)
- MODELLER (3)
- NAMD2 (3)
- OVITO (3)
- PLUMED (3)
- PyMOL (3)
- ACPYPE (2)
- AdResS (2)
- AutoDock Vina (2)
- CMA-ES (2)
- KEGG (2)
- MCELL (2)
- METIS (2)
- MarDyn (2)
- Matlab (2)
- P-LINCS (2)
- PDB2PQR (2)
- PETSc (2)
- PRMLT (2)
- Pfam (2)
- Python (2)
- Q-SiteFinder (2)
- QUESO (2)
- SWISS-MODEL (2)
- Stan (2)
- TINKER (2)
- Trilinos (2)
- ZIBgridfree (2)
- iRNAm5C-PseDNC (2)
- pLoc-mEuk (2)
- pLoc-mPlant (2)
- ABC-SubSim (1)
- ACEMD (1)
- AFMPB (1)
- AMINO (1)
- APCluster (1)
- AUTO-MUTE (1)
- AdaGrad (1)
- Adam (1)
- AirSim (1)
- Algorithm 247 (1)
- Alya (1)
- Amira (1)
- Apbsmem (1)
- AutoPas (1)
- BLAST (1)
- BRENT (1)
- BUGS (1)
- BayesDA (1)
- BigDFT (1)
- Bio-PEPA (1)
- BioJava (1)
- BioShape (1)
- Blaze-DEMGPU (1)
- Boost (1)
- Boost C++ Libraries (1)
- CCP4 (1)
- CHARM++ (1)
- CHARMM-GUI (1)
- CHARMM36m (1)
- COFACTOR (1)
- COILCHECK (1)
- COSMOS (1)
- CUPSAT (1)
- Cellware (1)
- ChEMBL (1)
- Chaospy (1)
- Chombo (1)
- ClustalW (1)
- Code_Aster (1)
- Code_Saturne (1)
- DAKOTA (1)
- DEMMAT (1)
- DL_MESO (1)
- DelPhi (1)
- DesParO (1)
- DifferentialEquations.jl (1)
- Dizzy (1)
- Doxygen (1)
- DrugscorePPI (1)
- and 151 more Software Packages
