scholarly journals An adaptive multi-level simulation algorithm for stochastic biological systems

2015 ◽  
Vol 142 (2) ◽  
pp. 024113 ◽  
Author(s):  
C. Lester ◽  
C. A. Yates ◽  
M. B. Giles ◽  
R. E. Baker
Keyword(s):  
Biological Systems ◽  
Simulation Algorithm ◽  
Multi Level

scholarly journals Rule-based multi-level modeling of cell biological systems

2011 ◽  
Vol 5 (1) ◽  
pp. 166 ◽  
Author(s):  
Carsten Maus ◽  
Stefan Rybacki ◽  
Adelinde M Uhrmacher
Keyword(s):  
Biological Systems ◽  
Rule Based ◽  
Multi Level

scholarly journals An Efficient GaMD Multi-Level Enhanced Sampling Strategy: Application to Polarizable Force Fields Simulations of Large Biological Systems

2021 ◽  
Author(s):  
Fréderic Célerse ◽  
Theo Jaffrelot-Inizan ◽  
Louis Lagardère ◽  
Olivier Adjoua ◽  
Pierre Monmarché ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Adaptive Sampling ◽  
Force Fields ◽  
Biological Systems ◽  
Sampling Strategy ◽  
Umbrella Sampling ◽  
Potential Of Mean Force ◽  
Enhanced Sampling ◽  
Polarizable Force Fields ◽  
Multi Level

We introduce a novel multi-level enhanced sampling strategy grounded on Gaussian accelerated Molecular Dynamics (GaMD). First, we propose a GaMD multi-GPUs-accelerated implementation within the Tinker-HP molecular dynamics package. We introduce the new "dual-water" mode and its use with the flexible AMOEBA polarizable force field.By adding harmonic boosts to the water stretching and bonding terms, it accelerates the solvent-solute interactions while enabling speedups thanks to the use of fast multiple--timestep integrators. To further reduce time-to-solution, we couple GaMD to Umbrella Sampling (US). The GaMD—US/dual--water approach is tested on the 1D Potential of Mean Force (PMF) of the solvated CD2--CD58 system (168000 atoms) allowing the AMOEBA PMF to converge within 1 kcal/mol of the experimental value. Finally, Adaptive Sampling (AS) is added enabling AS-GaMD capabilities but also the introduction of the new Adaptive Sampling--US--GaMD (ASUS-GaMD) scheme. The highly parallel ASUS--GaMD setup decreases time to convergence by respectively 10 and 20 times compared to GaMD-US and US. Overall, beside the acceleration of PMF computations, Tinker-HP now allows for the simultaneous use of Adaptive Sampling and GaMD-"dual water" enhanced sampling approaches increasing the applicability of polarizable force fields to large scale simulations of biological systems.

scholarly journals Extending the Multi-level Method for the Simulation of Stochastic Biological Systems

2016 ◽  
Vol 78 (8) ◽  
pp. 1640-1677 ◽  
Author(s):  
Christopher Lester ◽  
Ruth E. Baker ◽  
Michael B. Giles ◽  
Christian A. Yates
Keyword(s):  
Biological Systems ◽  
Level Method ◽  
Multi Level

scholarly journals The Development of a Three-Dimensional Material Point Method Computer Simulation Algorithm for Bullet Impact Studies

2010 ◽  
Vol 9 (2 and 3) ◽  
Author(s):  
M Connolly ◽  
E Maldonado ◽  
M Roth
Keyword(s):  
Computer Simulation ◽  
Biological Systems ◽  
Three Dimensional ◽  
Material Point Method ◽  
Material Point ◽  
Point Method ◽  
Three Dimensions ◽  
Simulation Algorithm ◽  
Two Dimensional ◽  
Impact Studies

The two-dimensional Material Point Method (MPM) algorithm outlined by Chen and Brannon has been extended to three dimensions. The development of the code is discussed as well as applications for simulating bullet impact on biological and non-biological systems.

Transmission Electron Microscopy of Protein Macromolecules

1971 ◽  
Vol 29 ◽  
pp. 424-425
Author(s):  
Henry S. Slayter
Keyword(s):  
Biological Systems ◽  
Metal Vapor ◽  
Resolving Power ◽  
Electron Microscopic ◽  
Chemical Methods ◽  
Molecular Weights ◽  
The Past ◽  
Physical Chemical ◽  
Transmission Electron

Electron microscopic methods have been applied increasingly during the past fifteen years, to problems in structural molecular biology. Used in conjunction with physical chemical methods and/or Fourier methods of analysis, they constitute powerful tools for determining sizes, shapes and modes of aggregation of biopolymers with molecular weights greater than 50, 000. However, the application of the e.m. to the determination of very fine structure approaching the limit of instrumental resolving power in biological systems has not been productive, due to various difficulties such as the destructive effects of dehydration, damage to the specimen by the electron beam, and lack of adequate and specific contrast. One of the most satisfactory methods for contrasting individual macromolecules involves the deposition of heavy metal vapor upon the specimen. We have investigated this process, and present here what we believe to be the more important considerations for optimizing it. Results of the application of these methods to several biological systems including muscle proteins, fibrinogen, ribosomes and chromatin will be discussed.

Freeze-fracture cytochemistry: A goal set by Russell Steere in 1957

1993 ◽  
Vol 51 ◽  
pp. 60-61
Author(s):  
Nicholas J Severs
Keyword(s):  
Chemical Nature ◽  
Biological Systems ◽  
Freeze Fracture ◽  
Structural Components ◽  
Major Goal ◽  
Membrane Biology ◽  
Routine Application ◽  
The Future ◽  
Freeze Etching

In his pioneering demonstration of the potential of freeze-etching in biological systems, Russell Steere assessed the future promise and limitations of the technique with remarkable foresight. Item 2 in his list of inherent difficulties as they then stood stated “The chemical nature of the objects seen in the replica cannot be determined”. This defined a major goal for practitioners of freeze-fracture which, for more than a decade, seemed unattainable. It was not until the introduction of the label-fracture-etch technique in the early 1970s that the mould was broken, and not until the following decade that the full scope of modern freeze-fracture cytochemistry took shape. The culmination of these developments in the 1990s now equips the researcher with a set of effective techniques for routine application in cell and membrane biology.Freeze-fracture cytochemical techniques are all designed to provide information on the chemical nature of structural components revealed by freeze-fracture, but differ in how this is achieved, in precisely what type of information is obtained, and in which types of specimen can be studied.

Seeking to uncover biology's chemical roots

2019 ◽  
Vol 3 (5) ◽  
pp. 435-443 ◽  
Author(s):  
Addy Pross
Keyword(s):  
Environmental Changes ◽  
Biological Systems ◽  
Significant Development ◽  
The Road ◽  
Physical Chemical ◽  
Systems Chemistry ◽  
Biological World ◽  
Inanimate Matter ◽  
The Origin Of Life ◽  
Opening Up

Despite the considerable advances in molecular biology over the past several decades, the nature of the physical–chemical process by which inanimate matter become transformed into simplest life remains elusive. In this review, we describe recent advances in a relatively new area of chemistry, systems chemistry, which attempts to uncover the physical–chemical principles underlying that remarkable transformation. A significant development has been the discovery that within the space of chemical potentiality there exists a largely unexplored kinetic domain which could be termed dynamic kinetic chemistry. Our analysis suggests that all biological systems and associated sub-systems belong to this distinct domain, thereby facilitating the placement of biological systems within a coherent physical/chemical framework. That discovery offers new insights into the origin of life process, as well as opening the door toward the preparation of active materials able to self-heal, adapt to environmental changes, even communicate, mimicking what transpires routinely in the biological world. The road to simplest proto-life appears to be opening up.

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