Peter Cifra | Slovak Academy of Sciences (original) (raw)

Papers by Peter Cifra

Netsu Sokutei, Jan 30, 1992

Biopolymers, Feb 25, 2022

We compute by molecular simulation the energy/entropic partition of the force in a stretched doub... 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.

Bulletin of the American Physical Society, Mar 6, 2014

Bulletin of the American Physical Society, 2016

We investigate suggested advantageous analysis in the linearization experiments with macromolecul... more We investigate suggested advantageous analysis in the linearization experiments with macromolecules confined in a stripe-like channel using Monte Carlo simulations. The enhanced chain extension in a stripe that is due to significant excluded volume interactions between monomers in two dimensions weakens on transition to experimentally feasible slitlike channel. Based on the chain extension-confinement strength dependence and the structure factor behavior for the chain in stripe we infer the excluded volume regime typical for two-dimensional systems. On transition to the slab geometry, the advantageous chain extension decreases and the Gaussian regime is observed for not very long semiflexible chains. The evidence for pseudo-ideality in confined chains is based on indicators such as the extension curves, variation of the extension with the persistence length or the structure factor. The slab behavior is observed when the stripe (originally of monomer thickness) reaches the thickness larger than cca 10nm in the third dimension. This maximum height of the slab to retain the advantage of the stripe is very low and this have implication for DNA linearization experiments. The presented analysis, however, has a broader relevance for confined polymers.

Journal of Physical Chemistry B, May 16, 2023

Nanoscale confinement of polymers in a cavity is central to a variety of biological and nanotechn... more Nanoscale confinement of polymers in a cavity is central to a variety of biological and nanotechnology processes. Using the discrete WLC model we simulate the compression of flexible and semiflexible polymers of linear and ring topology in a closed cavity. Simulation reveals that polymer pressure inside the cavity increases with the chain stiffness but is practically unaffected by the chain topology. For flexible polymers, the computed dependence of pressure on the cavity size and polymer concentration is consistent with the scaling behavior expected for bulk polymers in a good solvent. However, the scaling behavior of semiflexible polymers is only in partial agreement with the theory prediction, with discrepancies arising from a continuous transition between regimes in chains of moderate lengths. The computed segment density profiles endorse the propensity of semiflexible polymers to concentrate beneath the cavity surface and thus elevate the pressure. The compaction of polymers by compression into the disordered globule or growing toroidal structure is documented.

Die Makromolekulare Chemie

The concentration-dependent decrease of the entropy of polymer chains in polymer solutions is tre... 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.

Macromolecular Theory and Simulations, May 1, 1995

Lattice simulations of chains in good, theta and poor solvents were performed with an explicit in... more Lattice simulations of chains in good, theta and poor solvents were performed with an explicit incorporation of the excluded volume (chain thickness) into the model. The scaling power law for chain dimensions was found to apply in the theta and athermal states and to fail in the region below the theta state where collapsed chains with voids inside a globule occur. The solvent-induced globule-to-coil transition is transparently manifested by changes in the chain vector distribution functions. In the region of small and medium chain elongations, the simulation data can be fitted in the theta solvent by a Gaussian distribution function and in the athermal solvent by a function due to Oono et al. The stored elastic energy of the chains with fixed ends was calculated as a function of the chain-end displacement for fully flexible molecules in all three types of solvent and for poly(methy1ene).

Die Makromolekulare Chemie Rapid Communications

The Journal of Physical Chemistry B

We study the compression and extension response of single dsDNA molecules confined in cylindrical... 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.

The Journal of Chemical Physics

ACS Symposium Series, 2005

In polymeric systems such as polymer-particle colloid dispersions, composites and nano-composites... 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.

Macromolecular Symposia, 2010

Macromolecular Theory and Simulations, 2002

Langmuir, 1997

DOI to the publisher's website. • The final author version and the galley proof are versions of t... more DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. If the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the "Taverne" license above, please follow below link for the End User Agreement:

Journal of Polymer Science Part B: Polymer Physics, 1991

Local ordering in miscible binary polymer blends with strong attractive interactions between the ... more Local ordering in miscible binary polymer blends with strong attractive interactions between the two types of chains was investigated by computer simulation of allowable conformations on an incompressible cubic lattice. A tendency toward maximum ordering (in which chains pack in alternate parallel rows) is shown by the calculation of pair correlations and in "snapshots" of the mixtures. A specific directional interaction is not necessarily required for ordering. A comparison of these results with those recently obtained using mean-field theory is presented. The heat capacity of mixing was also calculated and found to be positive, with a value close to that reported experimentally.

Journal of Polymer Science Part B: Polymer Physics, 1992

Netsu Sokutei, Jan 30, 1992

Biopolymers, Feb 25, 2022

We compute by molecular simulation the energy/entropic partition of the force in a stretched doub... 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.

Bulletin of the American Physical Society, Mar 6, 2014

Bulletin of the American Physical Society, 2016

We investigate suggested advantageous analysis in the linearization experiments with macromolecul... more We investigate suggested advantageous analysis in the linearization experiments with macromolecules confined in a stripe-like channel using Monte Carlo simulations. The enhanced chain extension in a stripe that is due to significant excluded volume interactions between monomers in two dimensions weakens on transition to experimentally feasible slitlike channel. Based on the chain extension-confinement strength dependence and the structure factor behavior for the chain in stripe we infer the excluded volume regime typical for two-dimensional systems. On transition to the slab geometry, the advantageous chain extension decreases and the Gaussian regime is observed for not very long semiflexible chains. The evidence for pseudo-ideality in confined chains is based on indicators such as the extension curves, variation of the extension with the persistence length or the structure factor. The slab behavior is observed when the stripe (originally of monomer thickness) reaches the thickness larger than cca 10nm in the third dimension. This maximum height of the slab to retain the advantage of the stripe is very low and this have implication for DNA linearization experiments. The presented analysis, however, has a broader relevance for confined polymers.

Journal of Physical Chemistry B, May 16, 2023

Nanoscale confinement of polymers in a cavity is central to a variety of biological and nanotechn... more Nanoscale confinement of polymers in a cavity is central to a variety of biological and nanotechnology processes. Using the discrete WLC model we simulate the compression of flexible and semiflexible polymers of linear and ring topology in a closed cavity. Simulation reveals that polymer pressure inside the cavity increases with the chain stiffness but is practically unaffected by the chain topology. For flexible polymers, the computed dependence of pressure on the cavity size and polymer concentration is consistent with the scaling behavior expected for bulk polymers in a good solvent. However, the scaling behavior of semiflexible polymers is only in partial agreement with the theory prediction, with discrepancies arising from a continuous transition between regimes in chains of moderate lengths. The computed segment density profiles endorse the propensity of semiflexible polymers to concentrate beneath the cavity surface and thus elevate the pressure. The compaction of polymers by compression into the disordered globule or growing toroidal structure is documented.

Die Makromolekulare Chemie

The concentration-dependent decrease of the entropy of polymer chains in polymer solutions is tre... 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.

Macromolecular Theory and Simulations, May 1, 1995

Lattice simulations of chains in good, theta and poor solvents were performed with an explicit in... more Lattice simulations of chains in good, theta and poor solvents were performed with an explicit incorporation of the excluded volume (chain thickness) into the model. The scaling power law for chain dimensions was found to apply in the theta and athermal states and to fail in the region below the theta state where collapsed chains with voids inside a globule occur. The solvent-induced globule-to-coil transition is transparently manifested by changes in the chain vector distribution functions. In the region of small and medium chain elongations, the simulation data can be fitted in the theta solvent by a Gaussian distribution function and in the athermal solvent by a function due to Oono et al. The stored elastic energy of the chains with fixed ends was calculated as a function of the chain-end displacement for fully flexible molecules in all three types of solvent and for poly(methy1ene).

Die Makromolekulare Chemie Rapid Communications

The Journal of Physical Chemistry B

We study the compression and extension response of single dsDNA molecules confined in cylindrical... 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.

The Journal of Chemical Physics

ACS Symposium Series, 2005

In polymeric systems such as polymer-particle colloid dispersions, composites and nano-composites... 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.

Macromolecular Symposia, 2010

Macromolecular Theory and Simulations, 2002

Langmuir, 1997

DOI to the publisher's website. • The final author version and the galley proof are versions of t... more DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. If the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the "Taverne" license above, please follow below link for the End User Agreement:

Journal of Polymer Science Part B: Polymer Physics, 1991

Local ordering in miscible binary polymer blends with strong attractive interactions between the ... more Local ordering in miscible binary polymer blends with strong attractive interactions between the two types of chains was investigated by computer simulation of allowable conformations on an incompressible cubic lattice. A tendency toward maximum ordering (in which chains pack in alternate parallel rows) is shown by the calculation of pair correlations and in "snapshots" of the mixtures. A specific directional interaction is not necessarily required for ordering. A comparison of these results with those recently obtained using mean-field theory is presented. The heat capacity of mixing was also calculated and found to be positive, with a value close to that reported experimentally.

Journal of Polymer Science Part B: Polymer Physics, 1992

In polymeric systems such as polymer-particle colloid dispersions, composites and nano-composites... 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 ... 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).