RCUK Academic Research Fellow

School of Molecular and Cellular Biology

**Background**: *Life manifests itself through complex dynamics across many scales, from â€œwiggling and jiggling of atomsâ€ (protein folding) to transcription dynamics in gene regulatory networks, disease dynamics and population dynamics. Advances in experimental techniques resulted in availability of multidimensional, time-resolved data about dynamical processes. On the other hand, advances in computer hardware and simulation algorithms made it possible to obtain detailed dynamical picture of real-life biological processes on a computer. Computational experiments became a vital component of researches arsenal, as was highlighted by the recent Nobel prize awarded to three computational chemists.
The large size of datasets generated by computer simulations or experiments makes the development of automated analysis tools very important, practically and conceptually. In our lab we focus on the development of an original state of the art approach which focuses specifically on accurate description of the dynamics and its application to the analysis of in-silico and in-vitro data.*

**Contact**: Garstang 10.132, +44(0) 113 34 33141,

**You can read more about Dr Krivov's interests here:**

http://www.astbury.leeds.ac.uk/people/staff/staffpage.php?StaffID=SK

Quantitative analysis of complex biological dynamics.

- Free energy landscape analysis of realistic protein folding simulations.

- Faculty Graduate School
**FindaPhD**Project details:

**BIOL5172M** - Practical Bioinformatics

**BIOC1303** - Introductory Biochemistry: Problem Solving and Data Handling**BIOC2303** - Intermediate Biochemistry: Skills**BIOC3160** - Laboratory/Literature/Computing Research Project**BIOC3231/32 A** - Computational biology**BIOL2301** - Intermediate Skills for Biological Sciences**BIOL2301/03/05/3400/MICR2320** - Intermediate Skills - BIOL/MICR/Cell Biology of Human Disease**BIOL2301/03/05/3400/MICR2320/3343** - Intermediate Skills - BIOL/MICR/Cell Biology of Human Disease**BIOL5172M** - Practical Bioinformatics

**Group Leader **Dr Sergei Krivov (*RCUK Academic Research Fellow*)

Quantitative analysis of complex biological dynamics.

**Krivov SV** The free energy landscape analysis of protein (FIP35) folding dynamics. *J Phys Chem B* **115** 12315-12324, 2011

DOI:10.1021/jp208585r

View abstract

**Krivov SV** Numerical construction of the p(fold) (committor) reaction coordinate for a Markov process. *J Phys Chem B* **115** 11382-11388, 2011

DOI:10.1021/jp205231b

View abstract

**Krivov SV, Karplus M** Diffusive reaction dynamics on invariant free energy profiles *P NATL ACAD SCI USA* **105** 13841-13846, 2008

DOI:10.1073/pnas.0800228105

**Krivov SV, Muff S, Caflisch A, Karplus M** One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: New insights into the folding process *J PHYS CHEM B* **112** 8701-8714, 2008

DOI:10.1021/jp711864r

**Krivov SV, Karplus M** One-dimensional free-energy profiles of complex systems: Progress variables that preserve the barriers *J PHYS CHEM B* **110** 12689-12698, 2006

DOI:10.1021/jp060039b

**Krivov SV, Karplus M** Hidden complexity of free energy surfaces for peptide (protein) folding. *Proc Natl Acad Sci U S A* **101** 14766-14770, 2004

DOI:10.1073/pnas.0406234101

View abstract

**Krivov SV, Karplus M** Free energy disconnectivity graphs: Application to peptide models *J CHEM PHYS* **117** 10894-10903, 2002

DOI:10.1063/1.1517606

**Krivov SV** Protein folding free energy landscape along the committor - The optimal folding coordinate. *Journal of Chemical Theory and Computation*, 2018

DOI:10.1021/acs.jctc.8b00101

View abstract

**Klein M, Krivov SV, Ferrer AJ, Luo L, Samuel AD, Karplus M** Exploratory search during directed navigation in C. elegans and Drosophila larva. *eLife* **6**, 2017

DOI:10.7554/elife.30503

View abstract

**Banushkina PV, Krivov SV** Optimal reaction coordinates *Wiley Interdisciplinary Reviews: Computational Molecular Science* **6** 748-763, 2016

DOI:10.1002/wcms.1276

View abstract

**Banushkina PV, Krivov SV** Nonparametric variational optimization of reaction coordinates *Journal of Chemical Physics* **143**, 2015

DOI:10.1063/1.4935180

View abstract

**Banushkina PV, Krivov SV** Fep1d: A Script for the Analysis of Reaction Coordinates *Journal of Computational Chemistry* **36** 878-882, 2015

DOI:10.1002/jcc.23868

View abstract

**Banushkina PV, Krivov SV** High-resolution free energy landscape analysis of protein folding *Biochemical Society Transactions* **43** 157-161, 2015

DOI:10.1042/BST20140260

**Krivov SV, Fenton H, Goldsmith PJ, Prasad RK, Fisher J, Paci E** Optimal reaction coordinate as a biomarker for the dynamics of recovery from kidney transplant. *PLoS Computational Biology* **10**, 2014

DOI:10.1371/journal.pcbi.1003685

View abstract

**Tian P, Jónsson SA, Ferkinghoff-Borg J, Krivov SV, Lindorff-Larsen K, Irbäck A, Boomsma W** Robust estimation of diffusion-optimized ensembles for enhanced sampling *Journal of Chemical Theory and Computation* **10** 543-553, 2014

DOI:10.1021/ct400844x

View abstract

**Krivov SV** Method to describe stochastic dynamics using an optimal coordinate *Physical Review E: Statistical, Nonlinear, and Soft Matter Physics* **88**, 2013

DOI:10.1103/PhysRevE.88.062131

View abstract

**Banushkina PV, Krivov SV** High-Resolution Free-Energy Landscape Analysis ofα-Helical Protein Folding: HP35 and Its Double Mutant. *Journal of Chemical Theory and Computation* **9** 5257-5266, 2013

DOI:10.1021/ct400651z

View abstract

**Radou G, Enciso M, Krivov SV, Paci E** Modulation of a protein free-energy landscape by circular permutation *Journal of Physical Chemistry B* **117** 13743-13747, 2013

DOI:10.1021/jp406818t

View abstract

**Krivov SV** On reaction coordinate optimality *Journal of Chemical Theory and Computation* **9** 135-146, 2013

DOI:10.1021/ct3008292

View abstract

**Krivov SV** Optimal dimensionality reduction of complex dynamics: the chess game as diffusion on a free-energy landscape. *Phys Rev E Stat Nonlin Soft Matter Phys* **84** 011135-, 2011

DOI:10.1103/PhysRevE.84.011135

View abstract

**Krivov SV** Is Protein Folding Sub-Diffusive? *PLOS COMPUT BIOL* **6**, 2010

DOI:10.1371/journal.pcbi.1000921

**Cecchini M, Krivov SV, Spichty M, Karplus M** Erratum: Calculation of free-energy differences by confinement simulations. Application to peptide conformers (Journal of Physical Chemistry B (2009) 113B) *Journal of Physical Chemistry B* **114** 6763-, 2010

DOI:10.1021/jp102878c

**Cecchini M, Krivov SV, Spichty M, Karplus M** Calculation of Free-Energy Differences by Confinement Simulations. Application to Peptide Conformers *J PHYS CHEM B* **113** 9728-9740, 2009

DOI:10.1021/jp9020646

**Allen LR, Krivov SV, Paci E** Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations *PLOS COMPUT BIOL* **5**, 2009

DOI:10.1371/journal.pcbi.1000428

**Auer S, Miller MA, Krivov SV, Dobson CM, Karplus M, Vendruscolo M** Importance of metastable states in the free energy landscapes of polypeptide chains. *Phys Rev Lett* **99** 178104-, 2007

DOI:10.1103/PhysRevLett.99.178104

View abstract

**Palyanov AY, Krivov SV, Karplus M, Chekmarev SF** A lattice protein with an amyloidogenic latent state: Stability and folding kinetics *J PHYS CHEM B* **111** 2675-2687, 2007

DOI:10.1021/jp067027a

**Chekmarev SF, Krivov SV, Karplus M** Folding of ubiquitin: A simple model describes the strange kinetics *J PHYS CHEM B* **110** 8865-8869, 2006

DOI:10.1021/jp056799o

**Chekmarev SF, Krivov SV, Karplus M** Folding time distributions as an approach to protein folding kinetics *J PHYS CHEM B* **109** 5312-5330, 2005

DOI:10.1021/jp047012h

**Krivov SV** Hierarchical global optimization of quasiseparable systems: application to Lennard-Jones clusters. *Phys Rev E Stat Nonlin Soft Matter Phys* **66** 025701-, 2002

DOI:10.1103/PhysRevE.66.025701

View abstract

**Krivov SV, Chekmarev SF, Karplus M** Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide *Physical review letters* **88** 038101-, 2002

View abstract

**Krivov SV, Chekmarev SF, Karplus M** Potential energy surfaces and conformational transitions in biomolecules: a successive confinement approach applied to a solvated tetrapeptide. *Phys Rev Lett* **88** 038101-, 2002

DOI:10.1103/PhysRevLett.88.038101

View abstract

**Krivov SV, Chekmarev SF, Karplus M** Investigation of the potential surface of tetraalanine-peptide by sequentially locking the molecular dynamic trajectory of the system in attraction basins *J STRUCT CHEM+* **42** 877-881, 2001

**Chekmarev SF, Krivov SV** Confinement of the molecular dynamics trajectory to a specified catchment area on the potential surface *CHEM PHYS LETT* **287** 719-724, 1998

**Chekmarev SF, Krivov SV** Total and fractional densities of states from caloric relations *PHYS REV E* **57** 2445-2448, 1998