Interaction of antimicrobial peptides, BP100 and pepR, with model membrane systems as explored by brownian dynamics simulations on a coarse-grained model

Biopolymers ◽  
2012 ◽  
Vol 98 (4) ◽  
pp. 294-312 ◽  
Author(s):  
Carla S. Alves ◽  
Visvaldas Kairys ◽  
Miguel A. R. B. Castanho ◽  
Miguel X. Fernandes
Keyword(s):  
Antimicrobial Peptides ◽  
Brownian Dynamics ◽  
Model Membrane ◽  
Coarse Grained ◽  
Membrane Systems ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

scholarly journals Torsional behavior of chromatin is modulated by rotational phasing of nucleosomes

2014 ◽  
Vol 42 (15) ◽  
pp. 9691-9699 ◽  
Author(s):  
Gi-Moon Nam ◽  
Gaurav Arya
Keyword(s):  
Brownian Dynamics ◽  
Extreme Values ◽  
Strong Dependence ◽  
Critical Role ◽  
Coarse Grained ◽  
Naked Dna ◽  
Coarse Grained Model ◽  
Torsional Behavior ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations

Abstract Torsionally stressed DNA plays a critical role in genome organization and regulation. While the effects of torsional stresses on naked DNA have been well studied, little is known about how these stresses propagate within chromatin and affect its organization. Here we investigate the torsional behavior of nucleosome arrays by means of Brownian dynamics simulations of a coarse-grained model of chromatin. Our simulations reveal a strong dependence of the torsional response on the rotational phase angle Ψ0 between adjacent nucleosomes. Extreme values of Ψ0 lead to asymmetric, bell-shaped extension-rotation profiles with sharp maxima shifted toward positive or negative rotations, depending on the sign of Ψ0, and to fast, irregular propagation of DNA twist. In contrast, moderate Ψ0 yield more symmetric profiles with broad maxima and slow, uniform propagation of twist. The observed behavior is shown to arise from an interplay between nucleosomal transitions into states with crossed and open linker DNAs and global supercoiling of arrays into left- and right-handed coils, where Ψ0 serves to modulate the energy landscape of nucleosomal states. Our results also explain the torsional resilience of chromatin, reconcile differences between experimentally measured extension-rotation profiles, and suggest a role of torsional stresses in regulating chromatin assembly and organization.

scholarly journals Gated Binding of Ligands to HIV-1 Protease: Brownian Dynamics Simulations in a Coarse-Grained Model

2006 ◽  
Vol 90 (11) ◽  
pp. 3880-3885 ◽  
Author(s):  
Chia-En Chang ◽  
Tongye Shen ◽  
Joanna Trylska ◽  
Valentina Tozzini ◽  
J. Andrew McCammon
Keyword(s):  
Brownian Dynamics ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Hiv 1

scholarly journals A geometric criterion for the optimal spreading of active polymers in porous media

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christina Kurzthaler ◽  
Suvendu Mandal ◽  
Tapomoy Bhattacharjee ◽  
Hartmut Löwen ◽  
Sujit S. Datta ◽  
...  
Keyword(s):  
Porous Media ◽  
Brownian Dynamics ◽  
Optimal Transport ◽  
Fundamental Principle ◽  
Coarse Grained ◽  
Geometric Criterion ◽  
Coarse Grained Model ◽  
Dynamics Simulations ◽  
Run Lengths ◽  
Brownian Dynamics Simulations

AbstractEfficient navigation through disordered, porous environments poses a major challenge for swimming microorganisms and future synthetic cargo-carriers. We perform Brownian dynamics simulations of active stiff polymers undergoing run-reverse dynamics, and so mimic bacterial swimming, in porous media. In accord with experiments of Escherichia coli, the polymer dynamics are characterized by trapping phases interrupted by directed hopping motion through the pores. Our findings show that the spreading of active agents in porous media can be optimized by tuning their run lengths, which we rationalize using a coarse-grained model. More significantly, we discover a geometric criterion for the optimal spreading, which emerges when their run lengths are comparable to the longest straight path available in the porous medium. Our criterion unifies results for porous media with disparate pore sizes and shapes and for run-and-tumble polymers. It thus provides a fundamental principle for optimal transport of active agents in densely-packed biological and environmental settings.

A Finite Element-Based Coarse-Grained Model for Cell–Nanomaterial Interactions by Combining Absolute Nodal Coordinate Formula and Brownian Dynamics

2020 ◽  
Vol 88 (4) ◽  
Author(s):  
Teng Ma ◽  
Yuanpeng Liu ◽  
Guochang Lin ◽  
Changguo Wang ◽  
Huifeng Tan
Keyword(s):  
Finite Element ◽  
Brownian Dynamics ◽  
Lipid Membrane ◽  
Contact Region ◽  
Detection Algorithm ◽  
Polymer Chains ◽  
Coarse Grained ◽  
Absolute Nodal Coordinate ◽  
Coarse Grained Model ◽  
Dynamics Simulations

Abstract A fundamental understanding of the interactions between one-dimensional nanomaterials and the cell membrane is of great importance for assessing the hazardous effects of viruses and improving the performance of drug delivery. Here, we propose a finite element-based coarse-grained model to describe the cell entry of nanomaterials based on an absolute nodal coordinate formula and Brownian dynamics. The interactions between nanoparticles and lipid membrane are described by the Lennard–Jones potential, and a contact detection algorithm is used to determine the contact region. Compared with the theoretical and published experimental results, the correctness of the model has been verified. We take two examples to test the robustness of the model: the endocytosis of nanorods grafted with polymer chains and simultaneous entry of multiple nanorods into a lipid membrane. It shows that the model can not only capture the effect of ligand–receptor binding on the penetration but also accurately characterize the cooperative or separate entry of multiple nanorods. This coarse-grained model is computationally highly efficient and will be powerful in combination with molecular dynamics simulations to provide an understanding of cell–nanomaterial interactions.

scholarly journals Thermal fluctuations of haemoglobin from different species: adaptation to temperature via conformational dynamics

2012 ◽  
Vol 9 (76) ◽  
pp. 2845-2855 ◽  
Author(s):  
A. M. Stadler ◽  
C. J. Garvey ◽  
A. Bocahut ◽  
S. Sacquin-Mora ◽  
I. Digel ◽  
...  
Keyword(s):  
Body Temperature ◽  
Time Scale ◽  
Brownian Dynamics ◽  
Conformational Dynamics ◽  
Coarse Grained ◽  
Mean Square ◽  
Temperature Range ◽  
Dynamics Simulations ◽  
Brownian Dynamics Simulations ◽  
Average Body

Thermodynamic stability, configurational motions and internal forces of haemoglobin (Hb) of three endotherms (platypus, Ornithorhynchus anatinus ; domestic chicken, Gallus gallus domesticus and human, Homo sapiens ) and an ectotherm (salt water crocodile, Crocodylus porosus ) were investigated using circular dichroism, incoherent elastic neutron scattering and coarse-grained Brownian dynamics simulations. The experimental results from Hb solutions revealed a direct correlation between protein resilience, melting temperature and average body temperature of the different species on the 0.1 ns time scale. Molecular forces appeared to be adapted to permit conformational fluctuations with a root mean square displacement close to 1.2 Å at the corresponding average body temperature of the endotherms. Strong forces within crocodile Hb maintain the amplitudes of motion within a narrow limit over the entire temperature range in which the animal lives. In fully hydrated powder samples of human and chicken, Hb mean square displacements and effective force constants on the 1 ns time scale showed no differences over the whole temperature range from 10 to 300 K, in contrast to the solution case. A complementary result of the study, therefore, is that one hydration layer is not sufficient to activate all conformational fluctuations of Hb in the pico- to nanosecond time scale which might be relevant for biological function. Coarse-grained Brownian dynamics simulations permitted to explore residue-specific effects. They indicated that temperature sensing of human and chicken Hb occurs mainly at residues lining internal cavities in the β-subunits.

scholarly journals Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

2016 ◽  
Vol 472 (2186) ◽  
pp. 20150556 ◽  
Author(s):  
Radek Erban
Keyword(s):  
Molecular Dynamics ◽  
Differential Equations ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Brownian Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Computational Domain ◽  
Coarse Grained Model ◽  
Dynamics Simulations

Molecular dynamics (MD) simulations of ions (K + , Na + , Ca 2+ and Cl − ) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

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