Research Area/ Research Interest: Computational biophysics
Research Paper Topics for: Masters and PhD Thesis and publication
- Mathematical and computational modelling of skin biophysics: a review
- Single-molecule techniques in biophysics: a review of the progress in methods and applications
- Biomolecular simulation: a computational microscope for molecular biology
- Biophysical Reviews Special Issue call: Computational biophysics and structural biology of proteins—A Special Issue in honor of Prof. Haruki Nakamura’s 70th …
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- Algorithmic challenges in computational molecular biophysics
- Computational biochemistry and biophysics
- Biomolecular electrostatics and solvation: a computational perspective
- Biophysics at Waseda University
- On the on-line journal “Biophysics and Physicobiology (BPPB)”
- Computational strategies and challenges for using native ion mobility mass spectrometry in biophysics and structural biology
- Biophysics and systems biology
- CHARMM additive and polarizable force fields for biophysics and computer-aided drug design
- Speeding up parallel GROMACS on high‐latency networks
- On the pH‐optimum of activity and stability of proteins
- Computational membrane biophysics: From ion channel interactions with drugs to cellular function
- Computational Biophysics of the Skin
- Computational models of neuronal biophysics and the characterization of potential neuropharmacological targets
- Protein-protein docking: From interaction to interactome
- Advances in protein structure prediction and design
- Frontiers in Computational Biophysics: A Symposium in Honor of Martin Karplus
- Generalized correlation for biomolecular dynamics
- Coarse-graining methods for computational biology
- Biophysics in Kanazawa University
- Biophysics in Latin America
- Systems biophysics of gene expression
- Segregation of granular particles by mass, radius, and density in a horizontal rotating drum
- Computational biology of the heart: from structure to function
- Images as drivers of progress in cardiac computational modelling
- A strategy for integrative computational physiology
- From factors to actors: Computational sociology and agent-based modeling
- Biophysics of olfaction
- Salt rejection and water transport through boron nitride nanotubes
- Quantification of uncertainty in computational fluid dynamics
- Using Situs for the integration of multi-resolution structures
- Review of cellular biophysics and modeling: a primer on the computational biology of excitable cells
- Metal binding affinity and selectivity in metalloproteins: insights from computational studies
- Voxel-based computational models of real human anatomy: a review
- Computational cell biology: spatiotemporal simulation of cellular events
- Computational analysis of conserved RNA secondary structure in transcriptomes and genomes
- Computational methodologies for real-space structural refinement of large macromolecular complexes
- Sampling large conformational transitions: adenylate kinase as a testing ground
- Tonic excitation and inhibition of neurons: ambient transmitter sources and computational consequences
- The analysis of visual motion: From computational theory to neuronal mechanisms
- Reviews in computational chemistry
- Beyond bistability: biophysics and temporal dynamics of working memory
- Computational SNP analysis: current approaches and future prospects
- What has de novo protein design taught us about protein folding and biophysics?
- The ion channel inverse problem: neuroinformatics meets biophysics
- Computational Biophysics
- Forewords to the special issue “Progress of theoretical and computational biophysics—in honor of Professor Nobuhiro Go’s outstanding contribution on the occasion …
- Computational neuroimaging of human visual cortex
- Introduction to the Australian Society for Biophysics
- A tool written in Scala for preparation and analysis in MD simulation and 3D-RISM calculation of biomolecules
- Do all backbone polar groups in proteins form hydrogen bonds?
- Theoretical and computational models of biological ion channels
- Theoretical and Computational Biophysics Molecular electrostatic potentials from crystal diffraction: the neurotransmitter y-aminobutyric acid. R. FStewart and …
- Introduction to the Fast Multipole Method: Topics in Computational Biophysics, Theory, and Implementation
- RNA secondary structure: physical and computational aspects
- Novel computational approaches to polypharmacology as a means to define responses to individual drugs
- Bacterial Biophysics
- Systems biology in immunology: a computational modeling perspective
- Optimization in computational systems biology
- Neuronal energy consumption: biophysics, efficiency and evolution
- Interacting ions in biophysics: real is not ideal
- Knowledge-based computational methods for identifying or designing novel, non-homologous antimicrobial peptides
- In Silico Approaches for Novel Drug Discovery Against Coronavirus by Employing the Hybrid Molecular Technique: A Review
- Applications of NMR and computational methodologies to study protein dynamics
- The biophysics of regenerative repair suggests new perspectives on biological causation
- From biophysics to models of network function
- Advancing computational biophysics with Virtual Reality
- Biophysics of tumor microenvironment and cancer metastasis-a mini review
- Implications of synaptic biophysics for recurrent network dynamics and active memory
- The XLVII Winter School of the Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland;“Molecules, Pathways, and …
- Multi-scale computational modelling in biology and physiology
- Historical Series: Photosynthesis Unraveling Photosynthesis Step by Step: Four Decades of Research in Theoretical and Computational Biophysics
- Learning to model G-quadruplexes: current methods and perspectives
- Computational biology in the study of cardiac ion channels and cell electrophysiology
- Modelling, inference and big data in biophysics
- Implementing vertex dynamics models of cell populations in biology within a consistent computational framework
- Mathematical and computational techniques to deduce complex biochemical reaction mechanisms
- Emerging computational approaches for the study of protein allostery
- Biophysical and computational fragment-based approaches to targeting protein–protein interactions: applications in structure-guided drug discovery
- Cavitand complexes in aqueous solution: collaborative experimental and computational studies of the wetting, assembly, and function of nanoscopic bowls in water
- Phase singularities and filaments: simplifying complexity in computational models of ventricular fibrillation
- On the role of electrostatics in protein–protein interactions
- Biophysics of catch bonds
- Treasuring the computational approach in medicinal plant research
- Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging
- Parallel algorithms and distributed systems for computational biophysics
- Computational studies of protein–drug binding affinity changes upon mutations in the drug target
- … of related to fields of Computational and Modeling, Instrumentation and Electronics, Energy, Biophysics, and Geophysics. After tight peer-review process, 32 papers …
- Stability and robustness properties of bioelectric networks: A computational approach
- Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMRspectroscopy
- An integrated bioinformatics and computational biophysics approach to enterovirus surveillance and research
- Protein Lattices and Short-Term Memory: Studies in Computational Biophysics
- Special Issue on Molecular Biology and Biophysics of Eukaryotic Cells
- Computational fluid dynamics applied to cardiac computed tomography for noninvasive quantification of fractional flow reserve: scientific basis
- Oxidized phosphatidylcholines in membrane‐level cellular signaling: from biophysics to physiology and molecular pathology
- New face of Journal of Medical Physics and Biophysics: a reflection of new spirit from a new organization
- Computational studies of protein–drug binding affinity changes upon mutations in the drug target
- … of related to fields of Computational and Modeling, Instrumentation and Electronics, Energy, Biophysics, and Geophysics. After tight peer-review process, 32 papers …
- Stability and robustness properties of bioelectric networks: A computational approach
- Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMRspectroscopy
- An integrated bioinformatics and computational biophysics approach to enterovirus surveillance and research
- Protein Lattices and Short-Term Memory: Studies in Computational Biophysics
- Special Issue on Molecular Biology and Biophysics of Eukaryotic Cells
- Computational fluid dynamics applied to cardiac computed tomography for noninvasive quantification of fractional flow reserve: scientific basis
- Oxidized phosphatidylcholines in membrane‐level cellular signaling: from biophysics to physiology and molecular pathology
- New face of Journal of Medical Physics and Biophysics: a reflection of new spirit from a new organization
- Can we rely on computational predictions to correctly identify ligand binding sites on novel protein drug targets? Assessment of binding site prediction methods and a …
- Annual Review of Biophysics, 2016.
- Computations of standard binding free energies with molecular dynamics simulations
- Free energy of a trans-membrane pore calculated from atomistic molecular dynamics simulations
- Biophysics of serotonin and the serotonin1A receptor: fluorescence and dynamics
- Cardiac resynchronization: insight from experimental and computational models
- Contact rearrangements form coupled networks from local motions in allosteric proteins
- Multiscale computational models of complex biological systems
- Uncovering molecular processes in crystal nucleation and growth by using molecular simulation
- An efficient approach to converting three-dimensional image data into highly accurate computational models
- Modeling and simulation of protein–surface interactions: achievements and challenges
- Structural genomics: computational methods for structure analysis
- Computational Biophysics and Nanobiophotonics
- Recent Developments in Polarizable Molecular Dynamics Simulations of Electrolyte Solutions
- Computational principles of movement neuroscience
- 3DSig 2008: Structural Bioinformatics and Computational Biophysics Satellite
- COMPUTATIONAL BIOPHYSICS OF PROTEINS AND MEMBRANES
- Computational cell biology
- Final report for Conference Support Grant” From Computational Biophysics to Systems Biology-CBSB12″
- Understanding nucleic acid–ion interactions
- Electrophysiological properties of computational human ventricular cell action potential models under acute ischemic conditions
- Computational approaches for the dynamics of structure formation in self-assembling polymeric materials
- Milestoning: An efficient approach for atomically detailed simulations of kinetics in biophysics
- Computational vision and regularization theory
- Biophysics of channelrhodopsin
- Hybrid computational phantoms for medical dose reconstruction
- Biophysics of Computation: Information Processing in Single Neurons, by Christof Koch
- An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance
- 3DSIG 2010: The 6th Structural Bioinformatics and Computational Biophysics Meeting
- Strengthening Semaglutide-GLP-1R Binding Affinity via a Val27-Arg28 Exchange in the Peptide Backbone of Semaglutide: A Computational Structural Approach
- The many faces of halogen bonding: A review of theoretical models and methods
- Modeling water, the hydrophobic effect, and ion solvation
- The quantum chemical cluster approach for modeling enzyme reactions
- Biomolecular applications of Poisson–Boltzmann methods
- Mapping folding energy landscapes with theory and experiment
- Images as drivers of progress in cardiac computational modelling
- Early computational processing in binocular vision and depth perception
- A framework to establish credibility of computational models in biology
- Computational prediction of proteins sumoylation: a review on the methods and databases
- Bioelectrical control of positional information in development and regeneration: a review of conceptual and computational advances
- The IUPS human physiome project
- The IUPS Physiome Project: a framework for computational physiology
- Musculoskeletal-see-through mirror: Computational modeling and algorithm for whole-body muscle activity visualization in real time
- Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
- How the genome folds: the biophysics of four-dimensional chromatin organization
- A Comprehensive Analysis of Human CYP3A4 Crystal Structures as a Potential Tool for Molecular Docking-Based Site of Metabolism and Enzyme Inhibition Studies
- Consistency principle for protein design
- Computational prediction of protein–protein interactions
- Regional Biophysics Conference: RBC2018
- Simulation tools for particle-based reaction-diffusion dynamics in continuous space
- The role of protonation states in ligand-receptor recognition and binding
- Biophysical Journal and the Biophysics Community
- Traveling electrical waves in cortex: insights from phase dynamics and speculation on a computational role
- Computational tools for structure-based ligand design
- Neurophysiological and computational principles of cortical rhythms in cognition
- Computational neuroscience
- Emerging methods in protein co-evolution
- Toward computational systems biology
- Correlative approaches in single-molecule biophysics: A review of the progress in methods and applications
- Global dynamics of proteins: bridging between structure and function
- Computational thinking and thinking about computing
- The study of G‐protein coupled receptor oligomerization with computational modeling and bioinformatics
- Simulating complex intracellular processes using object-oriented computational modelling
- Editorial overview: Computational neuroscience Adrienne Fairhall and Christian Machens
- Computational modeling of realistic cell membranes
- Programming structured DNA assemblies to probe biophysical processes
- Cations as hydrogen bond donors: a view of electrostatic interactions in DNA
- Uncertainty quantification and polynomial chaos techniques in computational fluid dynamics
- Biomolecular modeling and simulation: a field coming of age
- Towards a computational reconstruction of the electrodynamics of premature and full term human labour
- Computational models of molecular self-organization in cellular environments
- A new decade for Biophysical Reviews and a look into the future of biophysics
- Biophysics of actin filament severing by cofilin
- Nonlinear dynamics of the complex multi-scale network
- RNA folding: conformational statistics, folding kinetics, and ion electrostatics
- Small-angle X-ray scattering from RNA, proteins, and protein complexes
- Energy functions in de novo protein design: current challenges and future prospects
- Folding of glycoproteins: toward understanding the biophysics of the glycosylation code
- Collective protein dynamics in relation to function
- Twenty years on: the impact of fragments on drug discovery
- Measuring the forces that control protein interactions
- The role of protein loops and linkers in conformational dynamics and allostery
- Preconditioning techniques in computational fluid dynamics
- Molecular dynamics simulations of biomolecules: long-range electrostatic effects
- Recent theoretical and computational advances for modeling protein–ligand binding affinities
- Noncovalent interactions in biochemistry
- SAXS studies of ion–nucleic acid interactions
- Mathematical and computational challenges in population biology and ecosystems science
- Experimental and computational methods in cardiovascular fluid mechanics
- Machine learning in genomic medicine: a review of computational problems and data sets
- The role of fragment-based and computational methods in polypharmacology
- A review of “perceptrons: An introduction to computational geometry≓
- Covalent mechanochemistry: theoretical concepts and computational tools with applications to molecular nanomechanics
- Image-based computational fluid dynamics modeling in realistic arterial geometries
- Computational techniques for the automated detection of mycobacterium tuberculosis from digitized sputum smear microscopic images: A systematic review
- Coupling of metabolic, second messenger pathways and insulin granule dynamics in pancreatic beta-cells: a computational analysis
- Computational rabbit models to investigate the initiation, perpetuation, and termination of ventricular arrhythmia
- Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems
- A cell-centered approach to developmental biology
- Role of conical intersections in molecular spectroscopy and photoinduced chemical dynamics
- Ion Conduction and Selectivity in K+ Channels
- Statistics and related topics in single-molecule biophysics
- Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design
- Electrostatic mechanisms of DNA deformation
- Advancing drug discovery through enhanced free energy calculations
- TRANSITION PATH SAMPLING: Throwing Ropes Over Rough Mountain Passes, in the Dark
- Single-molecule experiments in vitro and in silico
- Multiscale models of cardiac muscle biophysics and tissue remodeling in hypertrophic cardiomyopathies
- Annual Review of Biophysics, 2018
- Volume-averaged SAR in adult and child head models when using mobile phones: A computational study with detailed CAD-based models of commercial mobile …
- Advances in free-energy-based simulations of protein folding and ligand binding
- Phase behavior of multicomponent membranes: Experimental and computational techniques
- Emerging computational methods for the rational discovery of allosteric drugs
- Theoretical and computational studies of dendrimers as delivery vectors
- On the metrics and Euler-Lagrange equations of computational anatomy
- Molecular recognition and docking algorithms
- Experimental and computational studies of strain–conduction velocity relationships in cardiac tissue
- Computational prediction of flow-generated sound
- Generalized born models of macromolecular solvation effects
- GPU computing in medical physics: A review
- Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes
- Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs
- Natural image statistics and neural representation
- The computational anatomy of psychosis
- FPGA supercomputing platforms: A survey
- Biophysics and function of phosphatidic acid: a molecular perspective
- Computer simulations of enzyme catalysis: methods, progress, and insights
- Rabbit-specific computational modelling of ventricular cell electrophysiology: Using populations of models to explore variability in the response to ischemia
- Biomechanics and biophysics of cancer cells
- Graph convolutional networks for computational drug development and discovery
- Inhibitors of HIV-1 protease: a major success of structure-assisted drug design
- Ribozyme structures and mechanisms
- Theory and modeling of RNA structure and interactions with metal ions and small molecules
- Computational enzyme design
- The interface of protein structure, protein biophysics, and molecular evolution
