scholarly journals Compressing molecular dynamics trajectories: Breaking the one-bit-per-sample barrier

2016 ◽  
Vol 37 (20) ◽  
pp. 1897-1906 ◽  
Author(s):  
Jan Huwald ◽  
Stephan Richter ◽  
Bashar Ibrahim ◽  
Peter Dittrich
Keyword(s):  
Author(s):  
Bharti bharti ◽  
Debabrata Deb

We use molecular dynamics simulations to investigate the ordering phenomena in two-dimensional (2D) liquid crystals over the one-dimensional periodic substrate (1DPS). We have used Gay-Berne (GB) potential to model the...


2017 ◽  
Vol 24 (02) ◽  
pp. 1750019 ◽  
Author(s):  
A. HASSANI ◽  
A. MAKAN ◽  
K. SBIAAI ◽  
A. TABYAOUI ◽  
A. HASNAOUI

Homoepitaxial growth film for (001), (110) and (111) Ni substrates is investigated by means of molecular dynamics (MD) simulation. Embedded atom method (EAM) is considered to represent the interaction potential between nickel atoms. The simulation is performed at 300[Formula: see text]K using an incident energy of 0.06[Formula: see text]eV. In this study, the deposition process is performed periodically and the period, [Formula: see text], is relative to a perfect layer filling. The coverage rate of the actual expected level, [Formula: see text], can be considered a determinant for thin-film growth of nickel. The [Formula: see text] level is the most filled level during the deposition on (001) substrate, while it is the less filled one in the case of (111) substrate. Moreover, the upper level is the one which is responsible for the surface roughness and the appearance time of an upper layer may also be a factor influencing the surface roughness. The deposition on (111) substrate induces the most rigorous surface with a rapid appearance time of the upper layers. The [Formula: see text] layers are almost completely filled for all substrates. The [Formula: see text] and lower layers are completely filled for (001) and (110) substrates while for (111) substrate the completely filled layers are [Formula: see text] and lower ones.


1994 ◽  
Vol 72 (11-12) ◽  
pp. 909-912 ◽  
Author(s):  
A. V. Nemukhin ◽  
B. L. Grigorenko ◽  
G. B. Sergeev

A model for calculation of spectral shifts in small molecules due to matrix environments is developed. The approach is based on the one-electron approximation and combines methods of ab initio quantum chemistry, density functional theory, and molecular dynamics simulations. Applications to Na2Kr62 heteroclusters demonstrate that the model is capable of reproducing spectral shifts of opposite sign for the experimentally studied A–X and B–X transitions in Na2 trapped inside the Kr matrix.


2008 ◽  
Vol 19 (09) ◽  
pp. 1349-1358 ◽  
Author(s):  
R. SUMI ◽  
Z. NÉDA

A many-body system with co-existing attractive and repulsive interactions is considered on a ring. The competing interactions lead to a frustration similar with the one existing in Correlation Clustering (CC). The optimal mechanical equilibrium of the system is searched by molecular dynamics simulations. As a function of the disorder quenched in the interactions, the system exhibits the phase-transition recently reported in CC. The simulated system can be considered as a continuous and efficient approach to the otherwise discrete, NP hard CC problem.


Author(s):  
George W. Patrick ◽  
Charles Cuell ◽  
Raymond J. Spiteri ◽  
William Zhang

In the formalism of constrained mechanics, such as that which underlies the SHAKE and RATTLE methods of molecular dynamics, we present an algorithm to convert any one-step integration method to a variational integrator of the same order. The one-step method is arbitrary, and the conversion can be automated, resulting in a powerful and flexible approach to the generation of novel variational integrators.


Author(s):  
Peter Stallinga

In this research we tried to answer the question: How to optimize the total production of economy. For finding the answer we used two postulates: First, a worker is incentivated to work if it pays off. When in the income ranking the neighbor below earns less and the one above earns more the worker will work harder and produce more. The productivity of the worker is proportional to this ’derivative’ in the income curve. (Note: a worker’s salary is not assumed necessarily proportional to his productivity). The second postulate depends on who is in control of the production process. In highly-simplified naming: In capitalism, the capital takes the decisions, in a democracy the people do, by vote. We also simulated a dictatorial system in which decisions can be imposedby a (benevolent) dictator. We used these ingredients in evolutionary computation. Starting with an arbitrary initial distribution, we make random small changes to it and if the total production increases, a decision will be made whether to implement these changes. This procedure is repeated until the distribution is stable. Remarkably, the outcomes for ’democracy’ and ’capitalism’ are similar. Capitalism and democracy go hand-in-hand together: One person getting all income, two people working, and most not working and not receiving. These results are also analytically found. In ’communism’, nobody works and everybody perishes. In a ’dictatorial’ system we can optimize production for the benefit of the people, and come to the conclusion that the introduction of minimum wages is beneficial, and these should be 50% of the average income.


2021 ◽  
Author(s):  
Victor Padilla-Sanchez

COVID19 pandemic has disrupted our lives since December 2019 causing millions of infections and deaths worldwide. After more than a year we have vaccines that are effective in preventing the disease even though we are far from finished to vaccinate most of the population. Certain countries are doing better vaccinating people while others are far behind and if that is not enough new variants have appeared that put at risk our progress on defeating COVID19. The virus SARS-CoV-2 is mutating and many mutations change the spike glycoprotein which binds to the human receptor ACE2 sometimes making the virus more infectious and able to evade immunity. One virus variant of concern (VoC) is the one called delta which is becoming prevalent very quickly among new infections. The delta variant is a real threat for many people that are not vaccinated. Here I present molecular dynamics of the receptor binding domain in complex with its receptor ACE2 to shed light on the structural interactions that make this variant more dangerous.


2020 ◽  
Vol 978 ◽  
pp. 487-491
Author(s):  
Divya Singh ◽  
Avinash Parashar

In this article, molecular dynamics simulations have been performed to study the effect of crack on the tensile strength of a bicrystal of Zr. Bicrystal with a symmetric tilt grain boundary, with crack and without crack, are generated along [0001] tilt axis. This is further subjected to tensile loading and the stress strain response of the bicrystals with and without crack is studied. The strength of the bicrystal with crack is lower than the one without crack.


2020 ◽  
Vol 10 (23) ◽  
pp. 8504
Author(s):  
Christian J. Burnham ◽  
Zdenek Futera ◽  
Zlatko Bacic ◽  
Niall J. English

The one-dimensional Schrödinger equation, applied to the H2 intramolecular stretch coordinate in singly to quadruply occupied large cages in extended Type II (sII) hydrogen clathrate hydrate, was solved numerically herein via potential-energy scans from classical molecular dynamics (MD), employing bespoke force-matched H2–water potential. For both occupation cases, the resultant H–H stretch spectra were redshifted by ~350 cm−1 vis-à-vis their classically sampled counterparts, yielding semi-quantitative agreement with experimental Raman spectra. In addition, ab initio MD was carried out systematically for different cage occupations in the extended sII hydrate to assess the effect of differing intra-cage intrinsic electric field milieux on H–H stretch frequencies; we suggest that spatial heterogeneity of the electrostatic environment is responsible for some degree of peak splitting.


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