Fast Electrostatic Force and Moment Calculations in Multibody-Based Simulations of Coarse-Grained Biopolymers

2011 ◽  
Author(s):  
Mohammad Poursina ◽  
Jeremy Laflin ◽  
Kurt S. Anderson
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Force ◽  
Center Of Mass ◽  
Computational Cost ◽  
Field Approximation ◽  
The Body ◽  
Divide And Conquer ◽  
Coarse Grained ◽  
Coarse Grain

In molecular simulations, the dominant portion of the computational cost is associated with force field calculations. Herein, we extend the approach used to approximate long range gravitational force and the associated moment in spacecraft dynamics to the coulomb forces present in coarse grained biopolymer simulations. We approximate the resultant force and moment for long-range particle-body and body-body interactions due to the electrostatic force field. The resultant moment approximated here is due to the fact that the net force does not necessarily act through the center of mass of the body (pseudoatom). This moment is considered in multibody-based coarse grain simulations while neglected in bead models which use particle dynamics to address the dynamics of the system. A novel binary divide and conquer algorithm (BDCA) is presented to implement the force field approximation. The proposed algorithm is implemented by considering each rigid/flexible domain as a node of the leaf level of the binary tree. This substructuring strategy is well suited to coarse grain simulations of chain biopolymers using an articulated multibody approach.

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

2017 ◽  
Vol 146 (5) ◽  
pp. 054501 ◽  
Author(s):  
Julian Michalowsky ◽  
Lars V. Schäfer ◽  
Christian Holm ◽  
Jens Smiatek
Keyword(s):  
Force Field ◽  
Long Range ◽  
Electrostatic Interactions ◽  
Coarse Grained ◽  
Water Model ◽  
Martini Force Field

SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics

2015 ◽  
Vol 11 (2) ◽  
pp. 723-739 ◽  
Author(s):  
Leonardo Darré ◽  
Matías Rodrigo Machado ◽  
Astrid Febe Brandner ◽  
Humberto Carlos González ◽  
Sebastián Ferreira ◽  
...  
Keyword(s):  
Force Field ◽  
Long Range ◽  
Coarse Grained ◽  
Aqueous Solvation

A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)-block-poly(ε-caprolactone) (PEG-b-PCL) micelles

2020 ◽  
Vol 22 (41) ◽  
pp. 24028-24040
Author(s):  
Maryam S. Sadeghi ◽  
Mohammad Reza Moghbeli ◽  
William A. Goddard
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Force Field ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Coarse Grain ◽  
The Novel ◽  
Poly Ethylene Glycol ◽  
P Application ◽  
Poly Ethylene

Application of the novel quantum based coarse grained force field (CGq FF) for formation of a micelle from 250 chains of 2000 Dalton CG-MePEG23-b-PCL9 block copolymer in water at 310.15 K.

scholarly journals Calcium fluctuations drive morphological patterning at the onset of Hydra morphogenesis

2021 ◽  
Author(s):  
Erez Braun
Keyword(s):  
Long Range ◽  
Body Plan ◽  
The Body ◽  
Coarse Grained ◽  
Whole Body ◽  
Cylindrical Shape ◽  
Mature Animal ◽  
Spatial Correlations ◽  
Calcium Activity ◽  
Spatial Fluctuations

Morphogenesis in animal development involves significant morphological transitions leading to the emerging body plan of a mature animal. Understanding how the collective physical processes drive robust morphological patterning requires a coarse-grained description of the dynamics and the characterization of the underlying fields. Here I show that calcium spatial fluctuations serve as an integrator field of the electrical-mechanical processes of morphogenesis in whole-body Hydra regeneration and drive the morphological dynamics. We utilize external electric fields to control the developmental process and study a critical transition in morphogenesis, from the initial spheroidal shape of the tissue to an elongated cylindrical shape defining the body plan of a mature animal. Morphogenesis paused under external voltage is associated with a significant increase of the calcium activity compared with the activity supporting normal development. The enhanced calcium activity is characterized by intensified spatial fluctuations, extended spatial correlations across the tissue and faster temporal fluctuations. In contrast, the normal morphogenesis process is characterized by relatively moderate calcium fluctuation activity and restrained spatial correlations. Long-range communication however, is essential for development. Blocking gap-junctions halts morphogenesis by suppressing the long-range electrical communication, severely reducing the overall calcium activity and enhancing its localization in the tissue. Normal calcium activity is resumed following the wash of the blocker drug, leading to a morphological transition characterizing a normal regeneration process and the emergence of a mature animal. Our methodology of controlling morphogenesis by a physical electric field allows us to gain a global statistical view of the dynamics. It shows that the normalized calcium spatial fluctuations exhibit a universal shape distribution, across tissue samples and conditions, suggesting the existence of a global constrain over these fluctuations. Studying the correlations in space and time of the calcium fluctuation field at the onset of morphogenesis opens a new vista on this process and paints a picture of development analogous to a dynamical phase transition.

scholarly journals On the dynamical motion of a gyro in the presence of external forces

2017 ◽  
Vol 9 (2) ◽  
pp. 168781401769173 ◽  
Author(s):  
T. S. Amer
Keyword(s):  
Force Field ◽  
Initial Conditions ◽  
Equations Of Motion ◽  
Center Of Mass ◽  
The Body ◽  
Parameter Method ◽  
Newtonian Force ◽  
Principal Axes ◽  
External Forces ◽  
Newtonian Force Field

This work shed light on the motion of a symmetric rigid body (gyro) about one of its principal axes in the presence of a Newtonian force field besides a gyro moment in which its second component equals null. It is assumed that the body center of mass is shifted slightly relative to the dynamic symmetry axis. The governing equations of motion are investigated taking into account some initial conditions. The desired solutions of these equations are achieved in framework of the small parameter method. The periodic solutions for the case of irrational frequencies are investigated. Euler’s angles have been used to interpret the motion at any time. The geometrical representations of the obtained solutions and the phase plane schemas of these solutions are announced during several plots. Discussion of the results is presented to reinforce the importance of the considered gyro moment and the Newtonian force field. The significance of this problem is due to the framework of its several applications in different industries such as airplanes, submarines, compasses, spaceships, and guided missiles.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

Driving Torsion Scans with Wavefront Propagation

2020 ◽  
Author(s):  
Yudong Qiu ◽  
Daniel Smith ◽  
Chaya Stern ◽  
mudong feng ◽  
Lee-Ping Wang
Keyword(s):  
Potential Energy ◽  
Force Field ◽  
Degrees Of Freedom ◽  
Computational Cost ◽  
Initial Guess ◽  
Field Development ◽  
Force Field Development ◽  
Wavefront Propagation ◽  
Open Source Software Package

<div>The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.</div><div>Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.</div><div>To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.</div><div>However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.</div><div>In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.</div><div>The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.</div><div>The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.</div>

On the motion of bodies based on changes in the kinetic moment

2019 ◽  
Vol 20 (4) ◽  
pp. 267-275
Author(s):  
Yury N. Razoumny ◽  
Sergei A. Kupreev
Keyword(s):  
Center Of Mass ◽  
Stellar Dynamics ◽  
Elementary Particles ◽  
The Body ◽  
Accelerated Motion ◽  
Indirect Confirmation ◽  
Physical Principles ◽  
Two Bodies ◽  
Central Gravitational Field ◽  
Kinetic Moment

The controlled motion of a body in a central gravitational field without mass flow is considered. The possibility of moving the body in the radial direction from the center of attraction due to changes in the kinetic moment relative to the center of mass of the body is shown. A scheme for moving the body using a system of flywheels located in the same plane in near-circular orbits with different heights is proposed. The use of the spin of elementary particles is considered as flywheels. It is proved that using the spin of elementary particles with a Compton wavelength exceeding the distance to the attracting center is energetically more profitable than using the momentum of these particles to move the body. The calculation of motion using hypothetical particles (gravitons) is presented. A hypothesis has been put forward about the radiation of bodies during accelerated motion, which finds indirect confirmation in stellar dynamics and in an experiment with the fall of two bodies in a vacuum. The results can be used in experiments to search for elementary particles with low energy, explain cosmic phenomena and to develop transport objects on new physical principles.

scholarly journals A divide-and-conquer algorithm for quantum state preparation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Israel F. Araujo ◽  
Daniel K. Park ◽  
Francesco Petruccione ◽  
Adenilton J. da Silva
Keyword(s):  
Computational Cost ◽  
Quantum Circuit ◽  
Divide And Conquer ◽  
Computational Time ◽  
Quantum Computers ◽  
Dimensional Vector ◽  
Quantum Devices ◽  
Divide And Conquer Algorithm ◽  
Quantum State Preparation ◽  
Quantum Device

AbstractAdvantages in several fields of research and industry are expected with the rise of quantum computers. However, the computational cost to load classical data in quantum computers can impose restrictions on possible quantum speedups. Known algorithms to create arbitrary quantum states require quantum circuits with depth O(N) to load an N-dimensional vector. Here, we show that it is possible to load an N-dimensional vector with exponential time advantage using a quantum circuit with polylogarithmic depth and entangled information in ancillary qubits. Results show that we can efficiently load data in quantum devices using a divide-and-conquer strategy to exchange computational time for space. We demonstrate a proof of concept on a real quantum device and present two applications for quantum machine learning. We expect that this new loading strategy allows the quantum speedup of tasks that require to load a significant volume of information to quantum devices.

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