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{{short description|Molecular dynamics modelling software}} {{Infobox software ...

...e done using sampling methods like [[molecular dynamics]] or [[Monte Carlo molecular modeling|Monte Carlo]] simulations at different states along the reaction c == Software == ...

...sics]], mainly in the field of molecular simulation (including [[molecular dynamics]] ('''MD''') and [[Monte Carlo method|Monte Carlo]] ('''MC''') simulations) ...al elevation: A method for improving the searching properties of molecular dynamics simulation ...

{{Infobox software ...dynamic response, as well as time reversible Born Oppenheimer [[Molecular Dynamics]] (MD). ...

{{Short description|Molecular dynamics simulation software}} {{Infobox software ...

...1755 | doi = 10.1002/wcms.1169 }}</ref> at various [[Granularity#Molecular dynamics|granularity]] levels. ...508375q }}</ref> An example is given by the chemomechanical dynamics of a molecular machine, such as [[Kinesin]].<ref name=":3" /><ref>{{cite journal | vauthor ...

...etropolis–Hastings algorithm]], with a [[Hamiltonian mechanics|Hamiltonian dynamics]] evolution simulated using a [[Time reversibility|time-reversible]] and vo ...quantitative disciplines, until in the mid-2010s the developers of [[Stan (software)|Stan]] implemented HMC in combination with [[automatic differentiation]].< ...

...title=On Identifiability of Nonlinear ODE Models and Applications in Viral Dynamics |journal=SIAM Review |language=en |volume=53 |issue=1 |pages=3–39 |doi=10.1 ...u |last1=Mao |first2=Jianping |last2=He |title=Unidentifiability of System Dynamics: Conditions and Controller Design |year=2023|class=eess.SY }}</ref> ...

..., along with chemical dynamics such as energy transfer rates and molecular dynamics with femtosecond time resolution. 2DIR experiments have only become possibl ...cal exchange, [[motional narrowing]], vibrational population transfer, and molecular reorientation on the sub-picosecond time scale. It has for example been use ...

...le: Equivalence of Wang–Landau Sampling, Statistical Temperature Molecular Dynamics, and Metadynamics." Journal of Chemical Theory and Computation 10.5 (2014): ...al elevation: A method for improving the searching properties of molecular dynamics simulation|issue=6|bibcode=1994JCAMD...8..695H|citeseerx=10.1.1.65.9176|s2c ...

...and bird: isolation by distance, by colonization or by adaptation?|journal=Molecular Ecology|date=2014|volume=23|issue=5|pages=1028–1039|doi=10.1111/mec.12672|p ...s of gene flow between populations were generated using population genetic software. Direct measures of dispersal were determined by quantifying the number of ...

...biochemical systems— A practical guide |journal=Progress in Biophysics and Molecular Biology |date=1979 |volume=33 |issue=2 |pages=99–187 |doi=10.1016/0079-6107 ...|title=Cell-signalling dynamics in time and space |journal=Nature Reviews Molecular Cell Biology |date=March 2006 |volume=7 |issue=3 |pages=165–176 |doi=10.103 ...

...method exponential time differencing (ETD) method that they used [[Maple (software)|Maple]] to derive. ...ic]] and [[Visual computing|visual]] computing, for example in [[molecular dynamics]],<ref>{{harvtxt|Michels|Desbrun|2015}}</ref> for [[Very-large-scale integr ...

...ein folding/unfolding and other conformational changes, and intermolecular dynamics such as reaction, binding, adsorption, and desorption that are particularly ...zia F, Zacharias M, Hugel T | title = Multidomain structure and correlated dynamics determined by self-consistent FRET networks | journal = Nature Methods | vo ...

...ible fluid dynamics''' ('''NICFD'''), or non ideal [[Compressible flow|gas dynamics]], is a branch of [[fluid mechanics]] studying the dynamic behavior of flui ...|first2=A. |date=2006 |title=Molecular interpretation of nonclassical gas dynamics of dense vapors under the van der Waals model |url=http://dx.doi.org/10.106 ...

...otation speed against time of [[Rhodobacter sphaeroides|R. Sphaeroides]] [[Molecular motors|flagellar motor]], and (d) red pixel intensity from a single scan li ...s=etal}}</ref>), and in [[biophysics]] (detecting state transitions in a [[molecular machine]] as recorded in time-position traces<ref name="traces">{{cite jour ...

...ang|first=Ziheng|title=Simulating molecular evolution|date=2014-05-15|work=Molecular Evolution|pages=418–441|publisher=Oxford University Press|doi=10.1093/acpro ...M | title = Relationships between gene trees and species trees | journal = Molecular Biology and Evolution | volume = 5 | issue = 5 | pages = 568–83 | date = Se ...

..., Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG | title = RuleMonkey: software for stochastic simulation of rule-based models | journal = BMC Bioinformati ...multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes | journal = BMC Systems Biology | volume = 4 | pages = 24 | date ...

...icability in pharmacology, physiology, nutrition, biochemistry, and system dynamics. It applies whenever a drug or nutrient is infused or ingested at a relativ ...rweight]].<ref>{{Cite journal |doi=10.1371/journal.pcbi.1000045 |title=The Dynamics of Human Body Weight Change |year=2008 |last1=Chow |first1=Carson C. |last2 ...

== Chemical aspects relevant to aquifer systems dynamics == ...asses is a valid alternative to the purpose of understanding the role of [[molecular structure]]s in determining the kind of physical and geochemical processes ...