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prof. dr hab. Cezary Czaplewski
Employment
- 2017 - 2021 assistant professor (part-time) at Faculty of Applied Physics and Mathematics
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total: 138
Catalog Publications
Year 2012
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1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins
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Molecular dynamics simulation of polymerization of p-xylylene
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Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides
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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics
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Year 2011
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1,4-DHP-lipid parameters and rod like micellae
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Coarse-Grained Models of Proteins: Theory and Applications
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Molecular dynamics simulations of the growth of poly (chloro-para-xylylene) films.
PublicationParylene C, poly(chloro-para-xylylene) is the most widely used member of the parylene family due to its excellent chemical and physical properties. In this work we analyzed the formation of the parylene C film using molecular mechanics and molecular dynamics methods. A five unit chain is necessary to create a stable hydrophobic cluster and to adhere to a covered surface. Two scenarios were deemed to take place. The obtained results...
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Molecular dynamics simulations of the growth of poly(chloro-para-xylylene) films
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Year 2010
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A DFT/TD DFT study of the structure and spectroscopic properties of 5-methyl-2-(8-quinolinyl)benzoxazole and its complexes with Zn(II) ion
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Implementation of Molecular Dynamics and Its Extensions with the Coarse-Grained UNRES Force Field on Massively Parallel Systems: Toward Millisecond-Scale Simulations of Protein Structure, Dynamics, and Thermodynamics
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Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field
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Potential of Mean Force of Association of Large Hydrophobic Particles: Toward the Nanoscale Limit
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Theoretical study of polymerization mechanism of p-xylylene based polymers
PublicationObliczenia kwantowe mechanizmu polimeryzacji parylenów, opartych o cząsteczki p-ksylilenów. Praca zawiera wyniki szczegółowych obliczeń wszystkich etapów polimeryzacji, wnioski dotyczące znalezionych stanów kwantowych i energetyki poszczególnych etapów procesu.
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Theoretical Study of Polymerization Mechanism of p-Xylylene Based Polymers
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Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations
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Year 2009
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Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins
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Conformation-activity relationships of cyclo-constrained μ/5 opioid agonists derived from the N-terminal tetrapeptide segment of dermorphin/deltorphin
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Deltorphin analogs restricted via a urea bridge: structure and opioid activity
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Dynamics study on single and multiple β-sheets
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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Year 2008
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Computational techniques for efficient conformational sampling of proteins
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Conformation-activity relationships ofcyclo-constrained µ/δ opioid agonists derived from theN-terminal tetrapeptide segment of dermorphin/deltorphin
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Conformational studies of vasopressin and mesotocin using NMR spectroscopy and molecular modelling methods. Part II: studies in the SDS micelle
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Deltorphin analogs restricted via a urea bridge: structure and opioid activity
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Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
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Implementations of Nosé–Hoover and Nosé–Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain
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Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains
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Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
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Year 2007
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Dynamic Formation and Breaking of Disulfide Bonds in Molecular Dynamics Simulations with the UNRES Force Field
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Meta-computations on the CLUSTERIX Grid
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Modification and Optimization of the United-Residue (UNRES) Potential Energy Function for Canonical Simulations. I. Temperature Dependence of the Effective Energy Function and Tests of the Optimization Method with Single Training Proteins
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Molecular Simulations of Rhodopsin Tetrameter
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Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size
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Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. 3. Calculation and Parameterization of the Potentials of Mean Force of Pairs of Identical Hydrophobic Side Chains
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Year 2006
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A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low‐Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United‐Residue Force Field
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Molecular dynamics study of amyloid formation of two Abl-SH3 domain peptides
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Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
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The Protein Folding Problem
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Year 2005
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An efficient molecular docking using conformational space annealing
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Charge Loss in Gas-Phase Multiply Negatively Charged Oligonucleotides
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Comment on “Molecular Origin of Anticooperativity in Hydrophobic Association”
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Comparison of two approaches to potential of mean force calculations of hydrophobic association: particle insertion and weighted histogram analysis methods
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Molecular Origin of Anticooperativity in Hydrophobic Association
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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests
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Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC
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Reply to “Comment on ‘Molecular Origin of Anticooperativity in Hydrophobic Association'”
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Year 2004
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Erratum to “Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles” [Biophys. Chem. 105 (2003) 339–359]
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Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 1. Tests of the Approach Using Simple Lattice Protein Models
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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins
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