Peter Cifra
Slovak Academy of Sciences, Polymer Institute, Faculty Member
Research Interests:
Research Interests:
We compute by molecular simulation the energy/entropic partition of the force in a stretched double-stranded (ds)DNA molecule that is not yet available from the single-molecule measurements. Simulation using the coarse-grained wormlike... more
We compute by molecular simulation the energy/entropic partition of the force in a stretched double-stranded (ds)DNA molecule that is not yet available from the single-molecule measurements. Simulation using the coarse-grained wormlike chain (WLC) model predicts a gradual decrease in the internal (bending) energy of DNA at stretching. The ensuing negative energy contribution to force fU is outweighed by the positive entropy contribution fS . The ratio fU /f, used to assess the polymer elasticity, is about -1 at the moderate extension of DNA. At the high extension, the extra energy expenses due to the contour length elongation make the ratio fU /f less negative. The simulation findings of the hybrid energy/entropy nature of DNA elasticity at weak and moderate forces are supported by computations using the thermoelastic method mimicking the polymer experiments in bulk. It is contended that the observation of the negative energy elasticity in DNA can be generalized to other semiflexible polymers described by the WLC model.
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
The concentration-dependent decrease of the entropy of polymer chains in polymer solutions is treated by Monte Carlo simulation technique and by blob analysis. The results suggest the existence of a universal relation for this dependence... more
The concentration-dependent decrease of the entropy of polymer chains in polymer solutions is treated by Monte Carlo simulation technique and by blob analysis. The results suggest the existence of a universal relation for this dependence over a broad concentration range. Differences between the observed combinatorial entropy of the multichain system and the behaviour proposed by mean-field treatments as well as implications for treatments of the melting entropy of a polymer are pointed out.
Research Interests:
Research Interests:
Research Interests:
Research Interests:
We study the compression and extension response of single dsDNA molecules confined in cylindrical channels by means of Monte Carlo simulations. The elastic response of µm-sized DNA to the external force acting through the chain ends or... more
We study the compression and extension response of single dsDNA molecules confined in cylindrical channels by means of Monte Carlo simulations. The elastic response of µm-sized DNA to the external force acting through the chain ends or through the piston is markedly affected by the size of the channel. The interpretation of the force (f)-displacement (R) functions under quasi-one-dimensional confinement is facilitated by resolving the overall change of displacement ΔR into the confinement contribution ΔRD and the force contribution ΔRf. The external stretching of confined DNA results in a characteristic pattern of f-R functions involving their shift to the larger extensions due to the channel-induced pre-stretching ΔRD. A smooth end-chain compression into loop-like conformations observed in moderately confined DNA can be accounted for by the relationship valid for a Gaussian chain in bulk. In narrow channels, the considerably pre-stretched DNA molecules abruptly buckle on compression by the backfolding into hairpins. On the contrary, the piston compression of DNA is characterized by a gradual reduction of the chain span S and by smooth f-S functions in the whole spatial range from the 3d near to 1d limits. The observed discrepancy between the shape of the f-R and f-S functions from two compression methods can be important for designing nanopiston experiments of compaction and knotting of single DNA in nanochannels.
Research Interests:
Research Interests:
In polymeric systems such as polymer-particle colloid dispersions, composites and nano-composites, clay-intercalates with polymers the geometrical confinement of macromolecules becomes one of crucial features influencing final properties.... more
In polymeric systems such as polymer-particle colloid dispersions, composites and nano-composites, clay-intercalates with polymers the geometrical confinement of macromolecules becomes one of crucial features influencing final properties. Confinement is a driving force also in characterization of macromolecules by liquid chromatography (LC). Macromolecular confinement near geometrical obstacle gives rise to a depletion of polymer concentration in the vicinity of wall and to the depletion force. We address the interplay of the confinement, the solvent quality, polymer adsorption, polymer concentration and its consequences for LC and colloid particle-polymer phase behavior. Particularly intriguing is the case of compensation of macromolecular exclusion and adsorption by the confining walls which marks the characteristic inversion of behavior in these fields.
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Research Interests:
Observation that DNA molecules in bacteriophage capsids preferentially form torus type of knots provided a sensitive gauge to evaluate various models of DNA arrangement in phage heads. Only models resulting in a preponderance of torus... more
Observation that DNA molecules in bacteriophage capsids preferentially form torus type of knots provided a sensitive gauge to evaluate various models of DNA arrangement in phage heads. Only models resulting in a preponderance of torus knots could be considered as close to reality. Recent studies revealed that experimentally observed enrichment of torus knots can be qualitatively reproduced in numerical simulations that include a potential inducing nematic arrangement of tightly packed DNA molecules within phage capsids. Here, we investigate what aspects of the nematic arrangement are crucial for inducing formation of torus knots. Our results indicate that the effective stiffening of DNA by the nematic arrangement not only promotes knotting in general but is also the decisive factor in promoting formation of DNA torus knots in phage capsids.
Research Interests:
The conformation and distribution of a flexible and semiflexible chain confined in an array of nanoposts arranged in parallel way in a square-lattice projection of their cross-section was investigated using coarse-grained molecular... more
The conformation and distribution of a flexible and semiflexible chain confined in an array of nanoposts arranged in parallel way in a square-lattice projection of their cross-section was investigated using coarse-grained molecular dynamics simulations. The geometry of the nanopost array was varied at the constant post diameter dp and the ensuing modifications of the chain conformation were compared with the structural behavior of the chain in the series of nanopost arrays with the constant post separation Sp as well as with the constant distance between two adjacent post walls (passage width) wp. The free energy arguments based on an approximation of the array of nanopost to a composite of quasi-channels of diameter dc and quasi-slits of height wp provide semiqualitative explanations for the observed structural behavior of both chains. At constant post separation and passage width, the occupation number displays a monotonic decrease with the increasing geometry ratio dc/wp or volum...
Research Interests:
Molecular simulations in nanochannels are used to explore the compression elasticity of ring polymers of stiffness (persistence length) similar to DNA. By combination with the parallel data for linear polymers, the effect of chain... more
Molecular simulations in nanochannels are used to explore the compression elasticity of ring polymers of stiffness (persistence length) similar to DNA. By combination with the parallel data for linear polymers, the effect of chain topology on their compression behavior is assessed. The results show that the ring polymers are much less bendable at longitudinal compression than the linear analogs. The chain span of linear polymers is continuously reduced at compression, whereas in ring polymers, an abrupt decrease of the span is observed. The simulation data elucidate this phenomenon as the buckling of a ring polymer into the double-folded hairpin. The shrinking ratio of sizes of the ring and linear chains shows a complex behavior much differing from the existing reports. The force-displacement functions for chains of both topologies at moderate confinement are very well accounted for by the mean-field Flory scheme. The theory predicts the difference in the mechanical stiffness of the ring and linear polymers in qualitative agreement with the simulation data. These findings are relevant to the compression behavior of semiflexible ring polymers under spatial constraints such as in nanofluidic experiments, disordered media, or cellular environment.
Research Interests:
Molecular simulations in nanochannels are used to explore the compression elasticity of ring polymers of stiffness (persistence length) similar to DNA. By combination with the parallel data for linear polymers, the effect of chain... more
Molecular simulations in nanochannels are used to explore the compression elasticity of ring polymers of stiffness (persistence length) similar to DNA. By combination with the parallel data for linear polymers, the effect of chain topology on their compression behavior is assessed. The results show that the ring polymers are much less bendable at longitudinal compression than the linear analogs. The chain span of linear polymers is continuously reduced at compression, whereas in ring polymers, an abrupt decrease of the span is observed. The simulation data elucidate this phenomenon as the buckling of a ring polymer into the double-folded hairpin. The shrinking ratio of sizes of the ring and linear chains shows a complex behavior much differing from the existing reports. The force-displacement functions for chains of both topologies at moderate confinement are very well accounted for by the mean-field Flory scheme. The theory predicts the difference in the mechanical stiffness of the ring and linear polymers in qualitative agreement with the simulation data. These findings are relevant to the compression behavior of semiflexible ring polymers under spatial constraints such as in nanofluidic experiments, disordered media, or cellular environment.
The free energy costs of extension of DNA molecules confined in square nanochannels are decoupled by means of Monte Carlo simulations into two modes attributable to confinement and external forces.
Research Interests:
The anisotropy of orientational correlations in DNA molecules confined in cylindrical channels is explored by Monte Carlo simulations using a coarse-grained model of double-stranded (ds) DNA. We find that the correlation function <... more
The anisotropy of orientational correlations in DNA molecules confined in cylindrical channels is explored by Monte Carlo simulations using a coarse-grained model of double-stranded (ds) DNA. We find that the correlation function < C(s)>(perpendicular to) in the transverse (confined) dimension exhibits a region of negative values in the whole range of channel sizes. Such a clear-cut sign of the opposite orientation of chain segments represents a microscopic validation of the Odijk deflection mechanism in narrow channels. At moderate-to-weak confinement, the negative < C(s)>(perpendicular to) correlations imply a preference of DNA segments for transverse looping. The inclination for looping can explain a reduction of stiffness as well as the enhanced knotting of confined DNA relative to that detected earlier in bulk at some channel sizes. Furthermore, it is shown that the orientational persistence length P or fails to convey the apparent stiffness of DNA molecules in channels. Instead, correlation lengths P-parallel to and P-perpendicular to in the axial and transverse directions, respectively, encompass the channel-induced modifications of DNA stiffness. Published by AIP Publishing.
Research Interests:
Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the... more
Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the two blocks of the confined diblock chain were investigated through a comparison of their size, structure, and penetration among nanoposts with the corresponding separate chains. The geometry of a nanopost array was varied at constant post separation or at constant width of the passage between nanoposts. The size of a single interstitial volume was comparable to or smaller than the size of the diblock chain. A comparison of the blocks with their separate analogous chains revealed that the mutual interactions between the blocks were shielded by the nanoposts and, thus, the blocks behaved independently. At constant passage width, competitive effects of the axial chain extension in interstitial volumes and the lateral chain expansion among interstitial...
Research Interests:
Equilibrium conformation of a semiflexible macromolecule in an array of nanoposts exhibits a non-monotonic behavior both at variation of the chain stiffness and increased crowding imposed by nanoposts. This is a result of the competition... more
Equilibrium conformation of a semiflexible macromolecule in an array of nanoposts exhibits a non-monotonic behavior both at variation of the chain stiffness and increased crowding imposed by nanoposts. This is a result of the competition between the axial chain extension in channel-like interstitial volumes between nanoposts and the chain partitioning among these volumes. The approximation of a nanopost array as a combination of a quasi-channel and a quasi-slit like geometry semi-qualitatively explains the behavior of a chain in the array. In this approximation, the interstitial spaces are viewed as being of the channel geometry, while the passages between two adjacent posts are viewed as being of the slit geometry. Interestingly, the stiffer chains tend to penetrate more readily through the passage apertures, in the direction perpendicular to the post axes, and thus to occupy more interstitial volumes. This is consistent with the prediction of the free-energy penalty that is lower ...
Research Interests:
The combined effects of the channel asymmetry and the closed chain topology on the chain extension, structure factor, and the orientation correlations were studied using coarse-grained molecular dynamics simulations for moderate chain... more
The combined effects of the channel asymmetry and the closed chain topology on the chain extension, structure factor, and the orientation correlations were studied using coarse-grained molecular dynamics simulations for moderate chain lengths. These effects are related to applications in linearization experiments with a DNA molecule in nanofluidic devices. According to the aspect ratio, the channels are classified as a stripe or slabs. The chain segments do not have any freedom to move in the direction of the narrowest stripe size, being approximately the same size as the segment size. The chains of both ring and linear topologies are extended more in a stripe than in a slab; this effect is strengthened for a ring. For a ring in a stripe, the extension-confinement strength dependence leads to effective Flory exponents even larger than 3/4, which is characteristic for a self-avoiding two-dimensional chain. While the chain extension-confinement strength dependence for both topologies ...
Research Interests:
Research Interests:
Research Interests:
Research Interests:
ABSTRACT Lattice chains, chain length 200 monomers, generated by the Monte Carlo method, have been studied on a tetrahedral lattice. Real-chain features such as conformational restrictions, variable segment interaction and chain thickness... more
ABSTRACT Lattice chains, chain length 200 monomers, generated by the Monte Carlo method, have been studied on a tetrahedral lattice. Real-chain features such as conformational restrictions, variable segment interaction and chain thickness were assumed in the model. The chain vector density distribution function W(R) and the related changes in the Helmholtz energy were calculated as a function of the displacement of the chain ends, R. The force–displacement curves derived by this approach are non-linear with the shape depending on the solvent quality. The energy changes, accompanying the chain deformation, due to (a) conformational isomerization and (b) loss of segment contacts, were computed. In the model used (a) leads to a negative and (b) to a positive energetic contribution, fu, to the total tensile force, f. The mixed energy–entropy character of the single-chain deformation was demonstrated for some representative chains differing in excluded volume and flexibility.
Research Interests:
We studied the structure and dynamics of star-shaped polymers by means of coarse-grained molecular dynamics simulations and analysis of structural transitions of semi-flexible macromolecules confined in nano-channels. The conformation of... more
We studied the structure and dynamics of star-shaped polymers by means of coarse-grained molecular dynamics simulations and analysis of structural transitions of semi-flexible macromolecules confined in nano-channels. The conformation of star arms in narrow channels is given by the channel width, arm flexibility and number of arms aligned together in the given region along the channel. We focused on the conformation transition, where all arms are initially stretched in one direction of the narrow channel and were interested in the process of how individual arms escape into a free volume region of channel. We found that the escape transition does not proceed from arm ends but progresses by extension of a loop starting from the branch point; the arms escape in individual steps and the extension of arms depends on how many arms align in parallel in the channel.
Research Interests:
Research Interests:
Research Interests:
Research Interests:
ABSTRACT
Research Interests:
ABSTRACTMiscibility behavior in a binary polymer mixture composed of flexible and semiflexible chains has been examined by Monte Carlo simulations on a cubic lattice. It is shown that as the flexibility of one component in an initially... more
ABSTRACTMiscibility behavior in a binary polymer mixture composed of flexible and semiflexible chains has been examined by Monte Carlo simulations on a cubic lattice. It is shown that as the flexibility of one component in an initially miscible mixture of flexible chains of both kinds is reduced the miscibility of the system is not necessarily lost. In fact, flexible chains in the mixture can adjust to this situation and the equilibrium number of segmental contacts between the blend components is retained. The situation is changed in systems in which the loss of flexibility is coupled with an aggregation tendency of the semiflexible chains. The disparity between blend components due to the presence of orientational correlations between the semiflexible chains to a certain extent drives the system towards demixing. However, the dominant role in miscibility behavior in mixtures of flexible and semiflexible chains is played by intermolecular interactions between blend components.
ABSTRACT Stiff macromolecules entrapped in channels or spherical cavities undergo a shape transition on increasing confinement as shown by our investigation using molecular simulations. In channels this weak-to-strong confinement... more
ABSTRACT Stiff macromolecules entrapped in channels or spherical cavities undergo a shape transition on increasing confinement as shown by our investigation using molecular simulations. In channels this weak-to-strong confinement transition leads to extended conformations without the hairpin-like back-folding. In cavities, on decrease of cavity radius, the semiflexible chain in a disordered state starts to organize into the torus. This happens when the extent of confinement reaches the lower bound of macromolecular flexibility given by the minimal radius of chain curvature or the persistence length. As a common rule for both types of confinement the transition to the ordered structures is observed when the radius of cavity or cylindrical channel comes down to the persistence length of macromolecular chain. This simple geometric rule finds its application in various confinement situations of stiff bio-macromolecules either in micro channel experiments or real biophysical situation such as DNA in viral capsids.
Research Interests:
Research Interests:
Research Interests:
Chain extension along the channel vs. the confinement curves for the stripe-like channel (upper curve) and in the four slab-like channels of increasing thickness in the transition curves below.
Research Interests:
Research Interests:
In polymeric systems such as polymer-particle colloid dispersions, composites and nano-composites, clayintercalates with polymers the geometrical confinement of macromolecules becomes one of crucial features influencing final properties.... more
In polymeric systems such as polymer-particle colloid dispersions, composites and nano-composites, clayintercalates with polymers the geometrical confinement of macromolecules becomes one of crucial features influencing final properties. Confinement is a driving force also in characterization of macromolecules by liquid chromatography (LC). Macromolecular confinement near geometrical obstacle gives rise to a depletion of polymer concentration in the vicinity of wall and to the depletion force. We address the interplay of the confinement, the solvent quality, polymer adsorption, polymer concentration and its consequences for LC and colloid particle-polymer phase behavior. Particularly intriguing is the case of compensation of macromolecular exclusion and adsorption by the confining walls which marks the characteristic inversion of behavior in these fields.
The dimensional and structural properties of polymers confined into a cavity are computed by the Monte Carlo method as a function of the chain stiffness. The reduction of the size ratio < R(2)> / < R(g)(2)> close to 2, distinctive of... more
The dimensional and structural properties of polymers confined into a cavity are computed by the Monte Carlo method as a function of the chain stiffness. The reduction of the size ratio < R(2)> / < R(g)(2)> close to 2, distinctive of compact spheres, is observed at squeezing of chains into a capsule. The plots of the static structure factor S(q) computed for stiff chains show characteristic humps attributed to the toroidal structure. The orientation correlation function is found to be a very sensitive indicator of the globule - toroid transition in encapsulated chains. Evidence is presented that the toroidal morphology is formed in stiff polymers when the capsule radius approaches the chain persistence length (D similar to P).