The Net Advance of Physics

The Net Advance of Physics: BIOPHYSICS

BIOLOGICAL PHYSICS:

Types: EVOLUTION; GENETICS;
Type: BIOMECHANICS: see also Swimming:
- Finite Element Analysis in Biology Homepage of Biomesh.Org
- Water Movement in Vascular Plants: A Primer by Sanjay P. Sane and Amit K. Singh [Journal of the Indian Institute of Science 91, 233 (2011)]
- An introduction to the hydrodynamics of locomotion on small scales by Eric Lauga [Les Houches 2012]
- Collective motion of cells: from experiments to models by Elod Mehes and Tamas Vicsek [2014/03]
- The Hydrodynamics of Active Systems by Julia M. Yeomans [2015]
- Bacterial Hydrodynamics by Eric Lauga [2015/09]
- A Novice Guide towards Human Motion Analysis and Understanding by Ahmed Nabil Mohamed [2015/09]
- An Updated Review of Methods and Advancements in Microvascular Blood Flow Imaging by Cerine Lal and Martin J. Leahy [Microcirculation 23, 345 (2016)]
- Active Brownian Particles in Complex and Crowded Environments by Clemens Bechinger et al. [2016/02]
- A brief introduction to the model microswimmer Chlamydomonas reinhardtii by Raphaël Jeanneret et al. [2016/06]
- A Survey of Visual Analysis of Human Motion and Its Applications by Qifei Wang [2016/08]
- Human Mobility: Models and Applications by Hugo Barbosa-Filho et al. [2017/10] 126 pp.
- Fluid flows shaping organism morphology by Karen Alim [2018/01]
- Nobel Symposium 162: Microfluidics edited by Johan Elf et al. [2017/12]
- Modelling chemotaxis of microswimmers: from individual to collective behavior by Benno Liebchen and H. Löwen [2018/02]
- Mathematical models for chemotaxis and their applications in self-organisation phenomena by Kevin J. Painter [2018/06]
- Physical Models of Collective Cell Migration by Ricard Alert and Xavier Trepat [2019/05]
- The use of biophysical approaches to understand ciliary beating by P. Cicuta [2020/01]
- Recent advances in blood rheology: A review by A. N. Beris et al. [2021/09]
Type: COMPUTATIONAL:
- Computational Models For Epilepsy by Roxana A. Stephanescu et al. [2012/01]
- An Introduction to RNA Databases by Marc P. Hoeppner et al. [2012/06]
- Evolutionary Algorithms: Concepts, Designs, and Applications in Bioinformatics: Evolutionary Algorithms for Bioinformatics by Ka-Chun Wong [2015/08]
- Thirty eight things to do with live slime mould by Andrew Adamatzky [2015/12]
- Lecture notes on stochastic models in systems biology by Peter S. Swain [2016/07]
- Approximation and inference methods for stochastic biochemical kinetics - a tutorial review by David Schnoerr et al. [Journal of Physics A 50, 093001 (2017)]
- Fluid flows shaping organism morphology by Karen Alim [2018/01]
- Simulation of Morphogen and Tissue Dynamics by M. D. Peters et al. [2018/06]
- Algorithms for biosequence search: past, present and future by Gregory Kucherov [2018/08]
- Algorithmic Complexity in Computational Biology by Davide Cirillo and Alfonso Valencia [2018/11]
- Simulation and Inference Algorithms for Stochastic Biochemical Reaction Networks: From Basic Concepts to State-of-the-Art by David J. Warne et al. [2018/12]
- Deep Learning in Bioinformatics: Introduction, Application, and Perspective in Big Data Era by Yu Li et al. [2019/03]
- Physarum polycephalum: Smart network adaptation by M. Le Verge-Serandour and K. Alim [2023/06]
Type: ECOLOGY:
- Localized Structures in Dissipative Media: From Optics to Plant Ecology by Mustapha Tlidi et al. [2014/08]
- Statistical Mechanics of Ecological Systems: Neutral Theory and Beyond by Sandro Azaele et al. [2015/06]
Type: EMBRYOLOGY:
- A survey of mathematical models on somitogenesis by H. Song [2023/10]
Type: EPIDEMIOLOGY: Bagnoli 98/10;
- Statistical physics of vaccination by Zhen Wang et al. [Physics Reports 664, 1 (2016)]
- Basic stochastic transmission models and their inference by Tom Britton [2018/01]
- Tutorial: Deriving the Efficient Influence Curve for Large Models by Jonathan Levy [2019/03]
- Toward Epidemic Thresholds on Temporal Networks: A Review and Open Questions by Jack Leitch et al. [2019/10]
- Stochastic epidemics in a heterogeneous community by V. C. Tran [2020/04]
- Disease Detectives: Using Mathematics to Forecast the Spread of Infectious Diseases by H. Z. Brooks et al. [2020/07]
- The SIR model of an epidemic by W. G. Faris [2021/04]
- Recent advances in epidemic modeling: Non-Markov stochastic models and their scaling limits by R. Forien et al. [2021/06]
- A review of commonly used compartmental models in epidemiology by M. Mehdaoui [2021/10]
Type: HEARING:
- The physics of hearing: fluid mechanics and the active process of the inner ear by Tobias Reichenbach and A. J. Hudspeth [Reports on Progress in Physics 77, 7 (2014)]
Type: MEDICAL:
- Neutron Therapy in the 21st Century by Thomas K. Kroc and James S. Welsh [2014/09]
- Accelerators for Medical Applications by R. Bailey (ed.) [2015/06] CAS-CERN Accelerator School; 346 pp.
- Fundamentals and advances in magnetic hyperthermia by Elio Alberto Périgo et al. [Applied Physics Reviews 2, 041302 (2015)] 104 pp.
- An Updated Review of Methods and Advancements in Microvascular Blood Flow Imaging by Cerine Lal and Martin J. Leahy [Microcirculation 23, 345 (2016)]
- Histological coherent Raman imaging: a prognostic review by Marcus T. Cicerone and Charles H. Camp Jr. [2017/09]
- Recent Advances in Computational Modeling of Thrombosis by Sumith Yesudasan and Rodney D. Averett [2018/01]
- Advances in optical coherence tomography for dermatology by Olivier Levecq et al. [2018/04]
- Modeling water transport processes in dialysis by Marina V. Voinova [2018/05]
- Magnetic Nanoparticles in Nanomedicine by Kai Wu et al. [2018/11]
- The Tear Turnover and Tear Clearance Tests: A Review by Izabela K. Garaszczuk et al. [Expert Review of Medical Devices 15, 219 (2018)]
- Fractional Calculus in Pharmacokinetics by Pantelis Sopasakis et al. [Journal of Pharmacokinetics and Pharmacodynamics 45, 107 (2018)]
- Advances in Microwave Near-Field Imaging: Prototypes, Systems, and Applications by Wenyi Shao [2019/09]
- A review of complex-systems approaches to cancer networks by A. Uthamacumaran [2020/09]
- Mathematical models of leukæmia and its treatment: A review by S. Chulián et al. [2020/11]
- A review of mathematical and computational methods in cancer dynamics by A. Uthamacumaran and H. Zenil [2022/01]
- Positronium physics and biomedical applications by S. D. Bass et al. [2023/02]
Type: MOLECULAR:
- An Introduction to Biomolecular Simulations and Docking by Cameron Mura and Charles E. McAnany [2014/07]
- Approximation and inference methods for stochastic biochemical kinetics - a tutorial review by David Schnoerr et al. [Journal of Physics A 50, 093001 (2017)]
- Single-molecule techniques in biophysics: a review of the progress in methods and applications by Helen Miller et al. [2017/04]
- Single-molecule kinetics in living cells by Johan Elf and Irmeli Barkefors [2018/09]
- Simulation and Inference Algorithms for Stochastic Biochemical Reaction Networks: From Basic Concepts to State-of-the-Art by David J. Warne et al. [2018/12]
Type: MORPHOGENESIS:
- Simulation of Morphogen and Tissue Dynamics by M. D. Peters et al. [2018/06]
Type: OPTHAMOLOGY: Re: LASERS: Introductory: Conlan 98;
Type: RADIOLOGY:
- X-ray microtomography in biology by Ryuta Mizutani and Yoshio Suzuki [Micron 43, 104 (2016)]
- A Review of Tomographic Reconstruction Techniques for Computed Tomography by Sanam Assili [2018/08]
- Dose Delivery Concept and Instrumentation by Simona Giordanengo and Marco Donetti [2018/03]
Type: SYSTEMS:
- Key challenges facing data-driven multicellular systems biology by Paul Macklin [2018/06]
Aspects: AMPHIPHILIC MEMBRANES; BIOLOGICAL NETWORKS; BIOPOLYMERS; CHROMATIN; IMMUNE NETWORKS; NETWORKS in general; NEURAL NETS;
Aspects: BIOFILMS:
- The Physics of Biofilms -- An Introduction by Marco G. Mazza [Journal of Physics D 49,, 203001 (2016)]
Aspects: BIOSENSORS:
- Diamond for biosensor applications by C. E. Nebel et al. [2020/05]
- A review on plasmonic nano-biosensors for virus detection, with a focus on coronavirus by M. M. Hassan et al. [2020/12]
Aspects: CELLS:
- Cell biology: Networks, regulation, pathways by Gasper Tkacik and William Bialek [2007/12]
- Physics of adherent cells by Ulrich S. Schwarz and Samuel S. Safran [Reviews of Modern Physics 85, 1327 (2013)]
- Collective motion of cells: from experiments to models by Elod Mehes and Tamas Vicsek [2014/03]
- Criticality in Cell Differentiation by Indrani Bose and Mainak Pal [2016/12]
- 100 years after Smoluchowski: stochastic processes in cell biology by David Holcman and Zeev Schuss [2016/12]
- The statistical physics of active matter: from self-catalytic colloids to living cells by Étienne Fodor and M. Cristina Marchetti [2017/08]
- Protein Pattern Formation by Erwin Frey et al. [2018/01]
- Continuum models of collective cell migration by Shiladitya Banerjee and M. Cristina Marchetti [2018/05]
- Physics and modelling of intracellular diffusion by Svyatoslav Kondrat [2018/10]
- [Cell] Membrane-Mediated Interactions by Anne-Florence Bitbol et al. [2019/03]
- Physical Models of Collective Cell Migration by Ricard Alert and Xavier Trepat [2019/05]
- Key Biology You Should Have Learned in Physics Class: Using Ideal-Gas Mixtures to Understand Biomolecular Machines by Daniel M. Zuckerman [2019/06]
- The Recent Advances in the Mathematical Modelling of Human Pluripotent Stem Cells by L. E. Wadkin et al. [2019/09]
- Contour Models of Cellular Adhesion by Luca Giomi [2019/10]
- Living cells on the move by R. Alert and X. Trepat [2021/06]
Aspects: CHIRALITY:
- Recent Progress in Chirality Research Using Circularly Polarized Light by Tsubasa Fukue [2010/09]
Aspects: CRYSTALS:
- Residual Stress and Strain in Biocrystals by E. Seknazi and B. Pokroy [Advanced Materials 30, 1707263 (2018)]
Aspects: DELAYS:
- Introduction to [Biological Population] Delay Models and Their Wave Solutions by Majid Bani-Yaghoub [2017/01]
Aspects: DNA and RNA MOLECULES (& CELL NUCLEUS):
- Single DNA conformations and biological function by Ralf Metzler et al. [2006/09]
- Physical descriptions of the bacterial nucleoid at large scales, and their biological implications by Vincenzo G. Benza et al. [2012/04]
- An Introduction to RNA Databases by Marc P. Hoeppner et al. [2012/06]
- Flexibility of nucleic acids: from DNA to RNA by Bao Lei et al. [2015/09]
- Use of topology in physical problems by Somendra M. Bhattacharjee [2015/12]
- The physicist's guide to one of biotechnology's hottest new topics: CRISPR-Cas by Melia E. Bonomo and Michael W. Deem [2017/12]
- Recent Advances on the Non-Coherent Band Surgery Model for Site-Specific Recombination by Allison H. Moore and Mariel Vazquez [2018/10]
- Review on DNA Cryptography by Mandrita Mondal and Kumar S. Ray [2019/04]
- What do we know about DNA mechanics so far? by A. Aggarwal et al. [2020/06]
Aspects: ELECTROCARDIOGRAPHY:
- ECG Feature Extraction Techniques - A Survey Approach by S. Karpagachelvi et al. [Int'l J. Comp. Sci. & Info. Sec'ty. 8, (2010)]
Aspects: ENZYMES:
- Enzyme Kinetics at the Molecular Level by Arti Dua [Resonance 24, 297 (2019)]
Aspects: ION CHANNELS:
- Computing the Field in Proteins and Channels by Bob Eisenberg [J. Membrane Biol. 150, 1 (1996)]
- Crowded Charges in Ion Channels by Bob Eisenberg [2010/09]
- Ion Channels, Natural Nanovalves by Bob Eisenberg [2012/06]
Aspects: MIGRATION:
- Physical Models of Collective Cell Migration by Ricard Alert and Xavier Trepat [2019/05]
Aspects: MONTE CARLO METHODS:
- Markov-Chain Monte Carlo Methods for Simulations of Biomolecules by Bernd A. Berg [Springer Lecture Notes in Physics 736, 319 (2008)]
Aspects: NEUROLOGY: See also NEURAL NETS
- A primer on information theory, with applications to neuroscience by Felix Effenberger [2013/04]
- Burst [of neuron activity] detection methods by E. Cotterill and S. J. Eglen [2018/02]
- Modelling the correlated activity of neural populations: a review by Christophe Gardella et al. [2018/06]
- A Review on Understanding Brain, Memory Retention and Recall Processes Using EEG and fMRI Techniques by Qazi Emad-Ul-Haq et al. [2019/05]
- Review of Newman's Analytical Series [of articles] on Disk Electrodes by Boshuo Wang and James D. Weiland [2019/08] For neuroscientists unfamiliar with the electrochemistry literature.
- How is information transmitted in a nerve? by M. Peyrard [2020/08]
Aspects: ORIGINS OF LIFE:
- Origins of Life: A Problem for Physics by Sara I. Walker [2017/05]
Aspects: SEQUENCING: Speed 2003/04;
- Physical approaches to DNA sequencing and detection by Michael Zwolak and Massimiliano Di Ventra [2007/08]
- The physicist's guide to one of biotechnology's hottest new topics: CRISPR-Cas by Melia E. Bonomo and Michael W. Deem [2017/12]
Aspects: SIMULATIONS: Rodriguez 2006/06;
Aspects: SINGLE-MOLECULE EXPERIMENTS:
- Single-molecule experiments in biological physics: methods and applications by Felix Ritort [J. Phys. C 18, R531 (2006)]
- The Physics of Life: one molecule at a time by Mark C. Leake [2012/11]
Aspects: SOFT MATERIALS:
- Effective Interactions in Soft Materials by Alan R. Denton [2007/11]
- Stochastic thermodynamics, fluctuation theorems, and molecular machines by Udo Seifert [2012/05]
- The statistical physics of active matter: from self-catalytic colloids to living cells by Étienne Fodor and M. Cristina Marchetti [2017/08]
Aspects: SOLITONS:
- Localized Structures in Dissipative Media: From Optics to Plant Ecology by Mustapha Tlidi et al. [2014/08]
Aspects: VIRUSES:
- Mechanisms of virus assembly by Jason D. Perlmutter and Michael F. Hagan [2014/07]
Re: BAYESIAN STATISTICS:
- Approximation and inference methods for stochastic biochemical kinetics - a tutorial review by David Schnoerr et al. [Journal of Physics A 50, 093001 (2017)]
Re: CELLULAR AUTOMATA: Bagnoli 98/10;
Re: COMPLEXITY: Parisi 94/12;
- Criticality and dynamical scaling in living systems by Miguel A. Muñoz [2017/12]
- Algorithmic Complexity in Computational Biology by Davide Cirillo and Alfonso Valencia [2018/11]
Re: FRACTIONAL CALCULUS:
- Fractional Calculus in Pharmacokinetics by Pantelis Sopasakis et al. [Journal of Pharmacokinetics and Pharmacodynamics 45, 107 (2018)]
Re: HELICES: Cahill 2005/02;
Re: LASERS:
- Tricks of the Light: The Remarkable Power of Laser Tweezers to Dissect Complex Biological Questions by Mark C. Leake [2018/12]
Re: NOISE:
- The chaos within: exploring noise in cellular biology by Iain G. Johnston [Significance 9, 17 (2012)]
- Stochasticity or Noise in Biochemical Reactions by Zachary Fox and Brian Munsky [2017/08]
Re: p-ADIC MATHEMATICS:
- p-Adic Mathematical Physics: The First 30 Years by Branko Dragovich et al. [2017/05]
Re: PARTICLE ACCELERATORS:
- Medical Applications [of Particle Accelerators] by C. Biscari and L. Falbo [2013/08]
Re: PLASMAS:
- Plasma medicine: A brief introduction by M. Laroussi [2021/06]
- Cold Gas Plasma Sources and the Science behind their Applications in Biology and Medicine by M. Laroussi [2021/06]
Re: STATISTICAL MECHANICS:
- Chemotaxis: How a Small Organism Finds a Food Source by Andrea Schmidt [On Mehran Kardar's stat mech homepage at MIT] Random walk for high-school students.
- A First Exposure to Statistical Mechanics for Life Scientists: by Hernan G. Garcia et al. [2007/08]
- Non-equilibrium statistical mechanics: From a paradigmatic model to biological transport by T. Chou et al. [2011/10]
- Stochastic thermodynamics, fluctuation theorems, and molecular machines by Udo Seifert [2012/05]
- First Passage processes in cellular biology by Srividya Iyer-Biswas and Anton Zilman [2015/03]
- Lecture notes on stochastic models in systems biology by Peter S. Swain [2016/07]
- The statistical physics of active matter: from self-catalytic colloids to living cells by Étienne Fodor and M. Cristina Marchetti [2017/08]
- Bacterial growth: a statistical physicist's guide by Rosalind J. Allen and Bartlomiej Waclaw [2018/12]
- Simulation and Inference Algorithms for Stochastic Biochemical Reaction Networks: From Basic Concepts to State-of-the-Art by David J. Warne et al. [2018/12]
- Nonequilibrium physics in biology by X.-N. Fang et al. [2020/12]
Re: THERMODYNAMICS:
- Key Biology You Should Have Learned in Physics Class: Using Ideal-Gas Mixtures to Understand Biomolecular Machines by Daniel M. Zuckerman [2019/06]
Re: TURBULENCE: Ross 95+;

THE NET ADVANCE OF PHYSICS