Enhanced sampling of particular degrees of freedom in molecular systems based on adiabatic decoupling and temperature or force scaling

2011 ◽  
Vol 135 (10) ◽  
pp. 104106 ◽  
Author(s):  
Anna-Pitschna E. Kunz ◽  
Haiyan Liu ◽  
Wilfred F. van Gunsteren
Keyword(s):  
Degrees Of Freedom ◽  
Enhanced Sampling ◽  
Molecular Systems ◽  
Force Scaling

scholarly journals "Dividing and Conquering" and "Caching" in Molecular Modeling

2021 ◽  
Author(s):  
Xiaoyong Cao ◽  
Pu Tian
Keyword(s):  
Molecular Modeling ◽  
Degrees Of Freedom ◽  
Materials Science ◽  
Force Fields ◽  
Coarse Graining ◽  
Divide And Conquer ◽  
Collective Variables ◽  
Molecular Systems ◽  
State Models ◽  
Molecular Science

Molecular modeling is widely utilized in subjects including but not limited to physics, chemistry, biology, materials science and engineering. Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, Most of important methodological advancements in more than half century of molecule modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science based on force fields parameterization by coarse graining, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes "dividing and conquering" and/or "caching" in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but no transferability is available. Deep learning has been utilized to realize more efficient and accurate ways of "dividing and conquering" and "caching" along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science and a third class of algorithm that facilitates molecular modeling through partially transferable in resolution "caching" of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for "dividing and conquering" and "caching" in complex molecular systems.

scholarly journals Photo-Induced Coupled Nuclear and Electron Dynamics in the Nucleobase Uracil

2021 ◽  
Vol 9 ◽  
Author(s):  
Lena Bäuml ◽  
Thomas Schnappinger ◽  
Matthias F. Kling ◽  
Regina de Vivie-Riedle
Keyword(s):  
Laser Pulse ◽  
Degrees Of Freedom ◽  
Relaxation Mechanism ◽  
Electron Dynamics ◽  
Nuclear Dynamics ◽  
Molecular Systems ◽  
Ultrafast Relaxation ◽  
Long Time ◽  
Fast Electronic ◽  
Ultrashort Laser

Photo-initiated processes in molecules often involve complex situations where the induced dynamics is characterized by the interplay of nuclear and electronic degrees of freedom. The interaction of the molecule with an ultrashort laser pulse or the coupling at a conical intersection (CoIn) induces coherent electron dynamics which is subsequently modified by the nuclear motion. The nuclear dynamics typically leads to a fast electronic decoherence but also, depending on the system, enables the reappearance of the coherent electron dynamics. We study this situation for the photo-induced nuclear and electron dynamics in the nucleobase uracil. The simulations are performed with our ansatz for the coupled description of the nuclear and electron dynamics in molecular systems (NEMol). After photo-excitation uracil exhibits an ultrafast relaxation mechanism mediated by CoIn's. Both processes, the excitation by a laser pulse and the non-adiabatic relaxation, are explicitly simulated and the coherent electron dynamics is monitored using our quantum mechanical NEMol approach. The electronic coherence induced by the CoIn is observable for a long time scale due to the delocalized nature of the nuclear wavepacket.

scholarly journals Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables

2018 ◽  
Author(s):  
Z. Faidon Brotzakis ◽  
Michele Parrinello
Keyword(s):  
Degrees Of Freedom ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Computational Cost ◽  
Md Simulations ◽  
Conformational Transitions ◽  
Enhanced Sampling ◽  
Collective Variables ◽  
Simulation Based ◽  
Combined Data

AbstractProtein conformational transitions often involve many slow degrees of freedom. Their knowledge would give distinctive advantages since it provides chemical and mechanistic insight and accelerates the convergence of enhanced sampling techniques that rely on collective variables. In this study, we implemented a recently developed variational approach to conformational dynamics metadynamics to the conformational transition of the moderate size protein, L99A T4 Lysozyme. In order to find the slow modes of the system we combined data coming from NMR experiments as well as short MD simulations. A Metadynamics simulation based on these information reveals the presence of two intermediate states, at an affordable computational cost.

scholarly journals Liquid intrusion in and extrusion from non-wettable nanopores for technological applications

2021 ◽  
Vol 94 (8) ◽  
Author(s):  
Alberto Giacomello ◽  
Carlo Massimo Casciola ◽  
Yaroslav Grosu ◽  
Simone Meloni
Keyword(s):  
Degrees Of Freedom ◽  
Rare Event ◽  
Point Of View ◽  
Molecular Systems ◽  
Nanoporous Media ◽  
Conversion Materials ◽  
Microscopic Interpretation ◽  
And Control ◽  
Kinetics Of ◽  
Theoretical Results

AbstractIn this article, we review some recent theoretical results about intrusion and extrusion of non-wetting liquids in and out of cavities of nanotextured surfaces and nanoporous materials. Nanoscale confinement allows these processes to happen at conditions which significantly differ from bulk phase coexistence. In particular, the pressure at which a liquid penetrates in and exits from cavities is of interest for many technological applications such as energy storage, dissipation, and conversion, materials with negative compressibility, ion channels, liquid chromatography, and more. Notwithstanding its technological interest, intrusion/extrusion processes are difficult to understand and control solely via experiments: the missing step is often a simple theory capable of providing a microscopic interpretation of the results, e.g., of liquid porosimetry or other techniques used in the field, especially in the case of complex nanoporous media. In this context, simulations can help shedding light on the relation between the morphology of pores, the chemical composition of the solids and liquids, and the thermodynamics and kinetics of intrusion and extrusion. Indeed, the intrusion/extrusion kinetics is determined by the presence of free energy barriers and special approaches, the so-called rare event techniques, must be used to study these processes. Usually, rare event techniques are employed to investigate processes occurring in relatively simple molecular systems, while intrusion/extrusion concerns the collective dynamics of hundreds to thousands of degrees of freedom, the molecules of a liquid entering in or exiting from a cavity, which, from the methodological point of view, is itself a challenge.

scholarly journals Preface: Special Topic on Enhanced Sampling for Molecular Systems

2018 ◽  
Vol 149 (7) ◽  
pp. 072001 ◽  
Author(s):  
Alessandro Laio ◽  
Athanassios Z. Panagiotopoulos ◽  
Daniel M. Zuckerman
Keyword(s):  
Special Topic ◽  
Enhanced Sampling ◽  
Molecular Systems

scholarly journals “Dividing and Conquering” and “Caching” in Molecular Modeling

2021 ◽  
Vol 22 (9) ◽  
pp. 5053
Author(s):  
Xiaoyong Cao ◽  
Pu Tian
Keyword(s):  
Molecular Modeling ◽  
Degrees Of Freedom ◽  
Materials Science ◽  
Coarse Graining ◽  
Divide And Conquer ◽  
Collective Variables ◽  
Molecular Systems ◽  
Materials Science And Engineering ◽  
State Models ◽  
Molecular Science

Molecular modeling is widely utilized in subjects including but not limited to physics, chemistry, biology, materials science and engineering. Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, most important methodological advancements in more than half century of molecular modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes “dividing and conquering” and/or “caching” in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but results are not transferable. Deep learning has been utilized to realize more efficient and accurate ways of “dividing and conquering” and “caching” along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science. This framework is based on a third class of algorithm that facilitates molecular modeling through partially transferable in resolution “caching” of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for “dividing and conquering” and “caching” in complex molecular systems.

scholarly journals Two-dimensional electronic–vibrational sum frequency spectroscopy for interactions of electronic and nuclear motions at interfaces

2021 ◽  
Vol 118 (34) ◽  
pp. e2100608118
Author(s):  
Gang-Hua Deng ◽  
Yuqin Qian ◽  
Tong Zhang ◽  
Jian Han ◽  
Hanning Chen ◽  
...  
Keyword(s):  
Excited State ◽  
Excited States ◽  
Degrees Of Freedom ◽  
Two Dimensional ◽  
Strongly Coupled ◽  
Molecular Systems ◽  
Sum Frequency ◽  
Quantum Chemistry Calculations ◽  
Vibrational Sum Frequency Spectroscopy ◽  
Vibronic Couplings

Interactions of electronic and vibrational degrees of freedom are essential for understanding excited-states relaxation pathways of molecular systems at interfaces and surfaces. Here, we present the development of interface-specific two-dimensional electronic–vibrational sum frequency generation (2D-EVSFG) spectroscopy for electronic–vibrational couplings for excited states at interfaces and surfaces. We demonstrate this 2D-EVSFG technique by investigating photoexcited interface-active (E)-4-((4-(dihexylamino) phenyl)diazinyl)-1-methylpyridin-1- lum (AP3) molecules at the air–water interface as an example. Our 2D-EVSFG experiments show strong vibronic couplings of interfacial AP3 molecules upon photoexcitation and subsequent relaxation of a locally excited (LE) state. Time-dependent 2D-EVSFG experiments indicate that the relaxation of the LE state, S2, is strongly coupled with two high-frequency modes of 1,529.1 and 1,568.1 cm−1. Quantum chemistry calculations further verify that the strong vibronic couplings of the two vibrations promote the transition from the S2 state to the lower excited state S1. We believe that this development of 2D-EVSFG opens up an avenue of understanding excited-state dynamics related to interfaces and surfaces.

Sign in / Sign up

Export Citation Format

Share Document