Literature DB >> 24089712

Perspective: Reaches of chemical physics in biology.

Martin Gruebele1, D Thirumalai.   

Abstract

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.

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Year:  2013        PMID: 24089712      PMCID: PMC5942441          DOI: 10.1063/1.4820139

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  87 in total

1.  Genetic regulatory mechanisms in the synthesis of proteins.

Authors:  F JACOB; J MONOD
Journal:  J Mol Biol       Date:  1961-06       Impact factor: 5.469

2.  Promoter melting triggered by bacterial RNA polymerase occurs in three steps.

Authors:  Jie Chen; Seth A Darst; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2010-07-01       Impact factor: 11.205

Review 3.  Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

Authors:  Eugene Shakhnovich
Journal:  Chem Rev       Date:  2006-05       Impact factor: 60.622

4.  The energy landscapes and motions of proteins.

Authors:  H Frauenfelder; S G Sligar; P G Wolynes
Journal:  Science       Date:  1991-12-13       Impact factor: 47.728

5.  Return to the RNAi world: rethinking gene expression and evolution.

Authors:  Craig C Mello
Journal:  Cell Death Differ       Date:  2007-12       Impact factor: 15.828

6.  Inclusion of persistence length-based secondary structure in replica field theoretic models of heteropolymer freezing.

Authors:  Jeffrey K Weber; Vijay S Pande
Journal:  J Chem Phys       Date:  2013-09-28       Impact factor: 3.488

7.  Competition enhances stochasticity in biochemical reactions.

Authors:  Taylor Firman; Kingshuk Ghosh
Journal:  J Chem Phys       Date:  2013-09-28       Impact factor: 3.488

Review 8.  The protein folding problem.

Authors:  Ken A Dill; S Banu Ozkan; M Scott Shell; Thomas R Weikl
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

9.  Protein stability and folding kinetics in the nucleus and endoplasmic reticulum of eucaryotic cells.

Authors:  A Dhar; K Girdhar; D Singh; H Gelman; S Ebbinghaus; M Gruebele
Journal:  Biophys J       Date:  2011-07-20       Impact factor: 4.033

10.  Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation.

Authors:  Elijah Roberts; John E Stone; Zaida Luthey-Schulten
Journal:  J Comput Chem       Date:  2012-09-25       Impact factor: 3.376

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  3 in total

Review 1.  Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.

Authors:  Jessica Nasica-Labouze; Phuong H Nguyen; Fabio Sterpone; Olivia Berthoumieu; Nicolae-Viorel Buchete; Sébastien Coté; Alfonso De Simone; Andrew J Doig; Peter Faller; Angel Garcia; Alessandro Laio; Mai Suan Li; Simone Melchionna; Normand Mousseau; Yuguang Mu; Anant Paravastu; Samuela Pasquali; David J Rosenman; Birgit Strodel; Bogdan Tarus; John H Viles; Tong Zhang; Chunyu Wang; Philippe Derreumaux
Journal:  Chem Rev       Date:  2015-03-19       Impact factor: 60.622

2.  Optically trapping tumor cells to assess differentiation and prognosis of cancers.

Authors:  M Pradhan; S Pathak; D Mathur; U Ladiwala
Journal:  Biomed Opt Express       Date:  2016-02-19       Impact factor: 3.732

3.  Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.

Authors:  Fabio Sterpone; Philippe Derreumaux; Simone Melchionna
Journal:  J Chem Theory Comput       Date:  2015-04-14       Impact factor: 6.006

  3 in total

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