scholarly journals Multiscale simulation of molecular processes in cellular environments

2016 ◽  
Vol 374 (2080) ◽  
pp. 20160225 ◽  
Author(s):  
Mara Chiricotto ◽  
Fabio Sterpone ◽  
Philippe Derreumaux ◽  
Simone Melchionna
Keyword(s):  
Biological Systems ◽  
Multiscale Simulation ◽  
Multiscale Modelling ◽  
Coarse Grained ◽  
Multiscale Simulations ◽  
Molecular Processes ◽  
Mutual Exchange ◽  
Recent Advances ◽  
Aqueous Solvent

We describe the recent advances in studying biological systems via multiscale simulations. Our scheme is based on a coarse-grained representation of the macromolecules and a mesoscopic description of the solvent. The dual technique handles particles, the aqueous solvent and their mutual exchange of forces resulting in a stable and accurate methodology allowing biosystems of unprecedented size to be simulated. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’.

scholarly journals Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications

2019 ◽  
Vol 20 (15) ◽  
pp. 3774 ◽  
Author(s):  
Nidhi Singh ◽  
Wenjin Li
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Structure Prediction ◽  
Biological Systems ◽  
Conformational Dynamics ◽  
Multiscale Simulation ◽  
Coarse Grained ◽  
Hierarchical Level ◽  
Dynamics Simulations

Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.

scholarly journals Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexey Bondar ◽  
Olga Rybakova ◽  
Josef Melcr ◽  
Jan Dohnálek ◽  
Petro Khoroshyy ◽  
...  
Keyword(s):  
Biological Systems ◽  
Linear Dichroism ◽  
Quantitative Information ◽  
Living Cells ◽  
Software Tools ◽  
Model Systems ◽  
Membrane Properties ◽  
Polarization Microscopy ◽  
Molecular Processes ◽  
Wide Range

AbstractFluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However, quantitating and interpreting linear dichroism in biological systems has been laborious and unreliable. Here we present a set of open source ImageJ-based software tools that allow fast and easy linear dichroism visualization and quantitation, as well as extraction of quantitative information on molecular orientations, even in living systems. The tools were tested on model synthetic lipid vesicles and applied to a variety of biological systems, including observations of conformational changes during G-protein signaling in living cells, using fluorescent proteins. Our results show that our tools and model systems are applicable to a wide range of molecules and polarization-resolved microscopy techniques, and represent a significant step towards making polarization microscopy a mainstream tool of biological imaging.

scholarly journals Two-photon small-molecule fluorescence-based agents for sensing, imaging, and therapy within biological systems

2021 ◽  
Vol 50 (2) ◽  
pp. 702-734
Author(s):  
Luling Wu ◽  
Jihong Liu ◽  
Ping Li ◽  
Bo Tang ◽  
Tony D. James
Keyword(s):  
Small Molecule ◽  
Biological Systems ◽  
Two Photon ◽  
Small Molecule Probes ◽  
Recent Advances ◽  
Design Construction

In this tutorial review, we will explore recent advances for the design, construction and application of two-photon excited fluorescence (TPEF)-based small-molecule probes.

Therapeutic properties of organotin complexes with reference to their structural and environmental features

2017 ◽  
Vol 37 (2) ◽  
pp. 51-70 ◽  
Author(s):  
Muhammad Iqbal ◽  
Saqib Ali ◽  
Ali Haider ◽  
Nasir Khalid
Keyword(s):  
Mode Of Action ◽  
Therapeutic Potential ◽  
Biological Systems ◽  
Structural Features ◽  
Present Review ◽  
Environmental Features ◽  
Recent Advances ◽  
Target Sites ◽  
Therapeutic Properties ◽  
Modes Of Interaction

AbstractOrganotin complexes are being extensively studied and screened for their therapeutic potential. Although many recent advances and achievements in this field have been made, the exact mode of action of these complexes is yet to be unveiled. In the present review, an attempt has been made to correlate the therapeutic properties of organotin complexes with their structural features and the environment in which these interact with biological systems. The mechanism, various modes of interaction with biological systems, and physiological target sites of organotin complexes have been highlighted as well.

Multi-scale simulations of biological systems using the OPEP coarse-grained model

2018 ◽  
Vol 498 (2) ◽  
pp. 296-304 ◽  
Author(s):  
Fabio Sterpone ◽  
Sébastien Doutreligne ◽  
Thanh Thuy Tran ◽  
Simone Melchionna ◽  
Marc Baaden ◽  
...  
Keyword(s):  
Biological Systems ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Multi Scale

scholarly journals Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations

2013 ◽  
Vol 3 (2) ◽  
pp. 20120087 ◽  
Author(s):  
D. Groen ◽  
J. Borgdorff ◽  
C. Bona-Casas ◽  
J. Hetherington ◽  
R. W. Nash ◽  
...  
Keyword(s):  
High Performance ◽  
Multiscale Simulation ◽  
High Fidelity ◽  
Biomedical Domain ◽  
Multiscale Simulations ◽  
Total Execution Time ◽  
Stent Restenosis ◽  
Single Scale ◽  
Wide Range ◽  
In Stent Restenosis

Multiscale simulations are essential in the biomedical domain to accurately model human physiology. We present a modular approach for designing, constructing and executing multiscale simulations on a wide range of resources, from laptops to petascale supercomputers, including combinations of these. Our work features two multiscale applications, in-stent restenosis and cerebrovascular bloodflow, which combine multiple existing single-scale applications to create a multiscale simulation. These applications can be efficiently coupled, deployed and executed on computers up to the largest (peta) scale, incurring a coupling overhead of 1–10% of the total execution time.

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