Kirill Katsov
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[24] Biological and synthetic membranes: What can be learned from a coarse-grained description? M. Mueller, K. Katsov, M. Schick Physics Reports, in press (2006). DOWNLOAD
[23]  Defects and their removal in block copolymer thin film simulations A. W. Bosse, S. W. Sides, K. Katsov, C. J. García-Cervera, G. H. Fredrickson J. Poly. Sci. B, 44, 2495-2511 (2006). In recent years, there has been increased interest in using microphase-separated block copolymer thin films as submicrometer/suboptical masks in next generation semiconductor and magnetic media fabrication. With the goals of removing metastable defects in block copolymer thin film simulations and potentially examining equilibrium defect populations, we report on two new numerical techniques that can be used in field-theoretic computer simulations: (1) a spectral amplitude filter (SF) that encourages the simulation to relax into high symmetry states (representing zero defect states), and (2) different variants of force-biased, partial saddle point Monte Carlo algorithms that allow for barrier crossing toward lower energy defect-free states. Beyond their use for removing defects, the force-biased Monte Carlo algorithms will be seen to provide a promising tool for studying equilibrium defect populations. DOWNLOAD
[22]  The central role of line tension in the fusion of biological membranes M. Schick, K. Katsov,  M. Mueller Mol. Phys., 103, 3055-3059 (2005). Recent progress in the fusion of biological membranes is reviewed to highlight the central role played by the line tension, which permits exquisite control of the process. DOWNLOAD
[21]  Field theoretic study of bilayer membrane fusion: II. Mechanism of a stalk-hole complex K. Katsov, M. Mueller, M. Schick Biophys. J., 90, 915-926 (2006). We use self-consistent field theory to determine structural and energetic properties of intermediates and transition states involved in bilayer membrane fusion. In particular, we extend our original calculations from those of the standard hemifusion mechanism, which was studied in detail in the first paper of this series (1), to consider a possible alternative to it. This mechanism involves non-axial stalk expansion, in contrast to the axially symmetric evolution postulated in the classical mechanism. Elongation of the initial stalk facilitates the nucleation of holes and leads to destabilization of the fusing membranes via the formation of a stalk-hole complex. We study properties of this complex in detail, and show how transient leakage during fusion, previously predicted and recently observed in experiment, should vary with lipid architecture and tension. We also show that the barrier to fusion in the alternative mechanism is lower than that of the standard mechanism by a few kBT over most of the relevant region of system parameters, so that this alternative mechanism is a viable alternative to the standard pathway. We emphasize that any mechanism, such as this alternative one, which affects even modestly the line tension of a hole in a membrane affects greatly the ability of that membrane to undergo fusion. DOWNLOAD
[20]  Interfacial roughening induced by the reaction of end-functionalized polymers at a PS/P2VP interface: quantitaive analysis by DSIMS B. J. Kim, H. Kang, K. Char, K. Katsov, G. H. Fredrickson, E. J. Kramer Macromolecules, 38, 6106 (2005). The reaction of end-functionalized polymer chains at the melt interface between the immiscible polymers, polystyrene (PS) and poly(2-vinylpyridine) (P2VP), has been investigated experimentally. Diblock copolymers were formed at the interface by the reaction of amine end-functionalized deuterated PS with anhydride end-functionalized P2VP. The normalized interfacial excess  z*PS/Rg,PS) of the deuterium-labeled block copolymer was determined using dynamic secondary ion mass spectrometry (DSIMS). As ê increases, the interfacial tension decreases to zero, at which point the interface becomes unstable, inducing interfacial roughening by hydrodynamic flow of the homopolymers. Roughening was detected using scanning force microscopy (SFM) after removing the polystyrene with a selective solvent. Evidence of the interfacial instability was also observed by cross-sectional transmission electron microscopy (TEM). The length scale of the corrugation was around 15 nm, which was comparable to the diameter of diblock copolymer emulsified droplets found near the interface. For a short symmetric block copolymer (PS (4K)-P2VP (4K)), we observed that the interfacial roughening takes place above 0.9, in good agreement with the predictions of self-consistent mean-field theory. DOWNLOAD
[19]  Phase separation of saturated and mono-unsaturated lipids as determined from microscopic model R. Elliott, K. Katsov, M. Schick, I. Szleifer J. Chem. Phys., 122, 044904 (2005). A molecular model is proposed of a bilayer consisting of fully saturated dipalmitoylphosphatidylcholine (DPPC) and mono-unsaturated dioleoylphosphatidylcholine (DOPC). The model not only encompasses the constant density within the hydrophobic core of the bilayer, but also the tendency of chain segments to align. It is solved within self-consistent field theory. A model bilayer of DPPC undergoes a main-chain transition to a gel phase, while a bilayer of DOPC does not do so above zero degrees centigrade because of the double bond which disrupts order.We examine structural and thermodynamic properties of these membranes and find our results in reasonable accord with experiment. In particular, order-parameter profiles are in good agreement with NMR experiments. A phase diagram is obtained for mixtures of these lipids in a membrane at zero tension. The system undergoes phase separation below the main-chain transition temperature of the saturated lipid. Extensions to the ternary DPPC, DOPC, and cholesterol system are outlined. DOWNLOAD
[18]  Fusion of biological membranes K. Katsov, M. Mueller, M. Schick, Pramana - J. of Phys., 64, 1127-1134 (2005). The process of membrane fusion has been examined by Monte Carlo simulation, and is found to be very di®erent than the conventional picture. The differences in mechanism lead to several predictions, in particular that fusion is accompanied by transient leakage. This prediction has recently been verified. Self-consistent field theory is applied to examine the free energy barriers in the different scenarios. DOWNLOAD
[17]  Field theoretic study of bilayer membrane fusion: I. Hemifusion mechanism K. Katsov, M. Mueller, M. Schick Biophys. J., 87, 3277-3290 (2004). Self-consistent field theory is used to determine structural and energetic properties of metastable intermediates and unstable transition states involved in the standard stalk mechanism of bilayer membrane fusion. A microscopic model of flexible amphiphilic chains dissolved in hydrophilic solvent is employed to describe these self-assembled structures. We find that the barrier to formation of the initial stalk is much smaller than previously estimated by phenomenological theories. Therefore its creation it is not the rate-limiting process. The relevant barrier is associated with the rather limited radial expansion of the stalk into a hemifusion diaphragm. It is strongly affected by the architecture of the amphiphile, decreasing as the effective spontaneous curvature of the amphiphile is made more negative. It is also reduced when the tension is increased. At high tension the fusion pore, created when a hole forms in the hemifusion diaphragm, expands without bound. At very low membrane tension, small fusion pores can be trapped in a flickering metastable state. Successful fusion is severely limited by the architecture of the lipids. If the effective spontaneous curvature is not sufficiently negative, fusion does not occur because metastable stalks, whose existence is a seemingly necessary prerequisite, do not form at all. However if the spontaneous curvature is too negative, stalks are so stable that fusion does not occur because the system is unstable either to a phase of stable radial stalks, or to an inverted-hexagonal phase induced by stable linear stalks. Our results on the architecture and tension needed for successful fusion are summarized in a phase diagram. DOWNLOAD
[16]  Composite mesostructures by nano-confinement Y. Wu, G. Cheng, K. Katsov, S. W. Sides, J. Wang, J. Tang, G. H. Fredrickson, M. Moskovits, G. D. Stucky Nature Materials, 3, 816-822 (2004). In a physically confi ned environment, interfacial interactions, symmetry breaking, structural frustration and confi nement-induced entropy loss can play dominant roles in determining molecular organization. Here we present a systematic study of the confined assembly of silica–surfactant composite mesostructures within cylindrical nanochannels of varying diameters. Using exactly the same precursors and reaction conditions that form the two-dimensional hexagonal SBA-15 mesostructured thin fi lm, unprecedented silica mesostructures with chiral mesopores such as singleand double-helical geometries spontaneously form inside individual alumina nanochannels. On tightening the degree of confinement, a transition is observed in the mesopore morphology from a coiled cylindrical to a spherical cagelike geometry. Self-consistent fi eld calculations carried out to account for the observed mesostructures accord well with experiment. The mesostructures produced by confined syntheses are useful as templates for fabricating highly ordered mesostructured nanowires and nanowire arrays. DOWNLOAD
[15]  Coarse grained models for collective phenomena in membranes: Computer simulation of membrane fusion M. Mueller, K. Katsov, M. Schick J. Poly. Sci. B, 41, 1441-1450 (2003). We discuss the role coarse-grained models play in investigating collective phenomena in bilayer membranes and place them in the context of alternative approaches. By reducing the degrees of freedom and applying simple effective potentials, coarsegrained models can address the large time scales and length scales We discuss the role coarse-grained models play in investigating collective phenomena in bilayer membranes and place them in the context of alternative approaches. By reducing the degrees of freedom and applying simple effective potentials, coarsegrained models can address the large time scales and length scales. DOWNLOAD
[14]  A new mechanism of model membrane fusion determined from Monte Carlo simulation M. Mueller, K. Katsov, M. Schick Biophys. J., 85, 1611-1623 (2003). We have carried out extensive Monte Carlo simulations of the fusion of tense apposed bilayers formed by amphiphilic molecules within the framework of a coarse-grained lattice model. The fusion pathway differs from the usual stalk mechanism. Stalks do form between the apposed bilayers, but rather than expand radially to form an axial-symmetric hemifusion diaphragm of the trans leaves of both bilayers, they promote in their vicinity the nucleation of small holes in the bilayers. Two subsequent paths are observed. 1), The stalk encircles a hole in one bilayer creating a diaphragm comprised of both leaves of the other intact bilayer, which ruptures to complete the fusion pore. 2), Before the stalk can encircle a hole in one bilayer, a second hole forms in the other bilayer, and the stalk aligns and encircles them both to complete the fusion pore. Both pathways give rise to mixing between the cis and trans leaves of the bilayer and allow for transient leakage. DOWNLOAD
[13]  Theory of T-junctions and symmetric tilt grain boundaries in pure and mixed polymer systems Daniel Duque, K. Katsov, M. Schick J. Chem. Phys., 117, 10315-10320 (2002). We apply self-consistent-field theory to T junctions and symmetric tilt grain boundaries in block copolymer systems with and without the addition of homopolymer. We find that, in the absence of homopolymer, T junctions have a larger free energy per unit area than that of the symmetric tilt junctions with which they compete except for a range of angles between about 100° and 130°. With the addition of homopolymer, this range increases. These results are quite consistent with experiment. As the angle between grains increases towards 180°, the T junction undergoes a morphological change somewhat similar to that which occurs in symmetric tilt grain boundaries. At the onset of this change, the free energy per unit area decreases markedly. DOWNLOAD
[12]  Incorporating molecular scale structure into the van der Waals theory of the liquid-vapor interface K. Katsov, J. D. Weeks J. Phys. Chem. B, 106, 8429-8436 (2002). We have developed a new and general theory of nonuniform fluids that naturally incorporates molecular scale information into the classical van der Waals theory of slowly varying interfaces. Here the theory is applied to the liquid-vapor interface of a Lennard-Jones fluid. The method combines a molecular field treatment of the effects of unbalanced attractive forces with a locally optimal use of linear response theory to approximate fluid structure by that of the associated (hard sphere like) reference fluid. Our approach avoids many of the conceptual problems that arise in the classical theory and shows why capillary wave effects are not included in the theory. The general theory and a simplified version gives results for the interface profile and surface tension for states with different temperatures and potential energy cutoffs that compare very favorably with simulation data. DOWNLOAD
[11]  Molecular theory of hydrophobic mismatch between lipids and peptides Daniel Duque, Xiao-jun Li, K. Katsov, Michael Schick J. Chem. Phys., 116, 10478-10484 (2002). Effects of the mismatch between the hydrophobic length d, of transmembrane alpha helices of integral proteins and the hydrophobic thickness, Dh , of the membranes they span are studied theoretically utilizing a microscopic model of lipids. In particular, we examine the dependence of the period of a lamellar phase on the hydrophobic length and volume fraction of a rigid, integral, peptide. We find that the period decreases when a short peptide, such that d,Dh , is inserted. More surprising, we find that the period increases when a long peptide, such that d.Dh , is inserted. The effect is due to the replacement of extensible lipid tails by rigid peptide. As the peptide length is increased, the lamellar period continues to increase, but at a slower rate, and can eventually decrease. The amount of peptide which fails to incorporate and span the membrane increases with the magnitude of the hydrophobic mismatch ud2Dhu. We explicate these behaviors which are all in accord with experiment. Predictions are made for the dependence of the tilt of a single trans-membrane alpha helix on hydrophobic mismatch and helix density. DOWNLOAD
[10]  New mechanism of membrane fusion M. Mueller, K. Katsov, M. Schick J. Chem. Phys., 116, 2342-2345 (2002). We have carried out Monte Carlo simulation of the fusion of bilayers of single chain amphiphiles which show phase behavior similar to that of biological lipids. The fusion mechanism we observe is very different from the ‘‘stalk’’ hypothesis. Stalks do form on the first stage of fusion, but they do not grow radially to form a single bilayer diaphragm. Instead, stalk formation destabilizes the membranes and results in hole formation in the vicinity of the stalks. When holes in each bilayer nucleate spontaneously next to the same stalk, an incomplete fusion pore is formed. The fusion process is completed by propagation of the initial connection, the stalk, along the edges of the aligned holes. DOWNLOAD
[9]  On the mean field treatment of attractive interactions in nonuniform simple fluids K. Katsov, J. D. Weeks J. Phys. Chem. B, 105, 6738-6744 (2001). We study thermodynamic and structural properties of a Lennard-Jones liquid at a state very close to the triple point as the radius of a hard sphere solute is varied. Oscillatory profiles arise for small, molecular sized radii, whereas for large radii smooth interfaces with a “drying layer” of low vapor density near the solute are seen. We develop a quantitative theory for this process using a new mean field treatment where the effects of attractive interactions are described in terms of a self-consistently chosen effective single particle field. We modify the usual simple molecular field approximation for the effective field in a very natural way, so that exact results (consistent with a given accurate equation of state for the uniform fluid) arise in the “hydrostatic limit” of very slowly varying interfaces. Very good agreement with the results of computer simulations for a wide range of solute radii are found. DOWNLOAD
[8]  Density fluctuations and the structure of a nonuniform hard sphere fluid K. Katsov, J. D. Weeks Phys. Rev. Lett., 86, 440-443 (2001). We derive an exact equation for density changes induced by a general external field that corrects the hydrostatic approximation where the local value of the field is adsorbed into a modified chemical potential. Using linear response theory to relate density changes self-consistently in different regions of space, we arrive at an integral equation for a hard sphere fluid that is exact in the limit of a slowly varying field or at low density and reduces to the accurate Percus-Yevick equation for a hard core field. This and related equations give accurate results for a wide variety of fields. DOWNLOAD
[7]  Using mean field theory to determine the structure of uniform fluids K. Vollmayr-Lee, K. Katsov, J. D. Weeks J. Chem. Phys., 114, 416-425 (2001). The structure of a uniform simple liquid is related to that of a reference fluid with purely repulsive intermolecular forces in a self-consistently determined external reference field (ERF) . The ERF can be separated into a harshly repulsive part generated by the repulsive core of a reference particle fixed at the origin and a more slowly varying part arising from a mean field treatment of the attractive forces. We use a generalized linear response method to calculate the reference fluid structure, first determining the response to the smoother part of the ERF alone, followed by the response to the harshly repulsive part. Both steps can be carried out very accurately, as confirmed by computer simulations, and good agreement with the structure of the full Lennard-Jones fluid is found. DOWNLOAD
[6]  Determining liquid structure from the tail of the direct correlation function K. Katsov, J. D. Weeks J. Stat. Phys., 100, 107-134 (2000). In important early work, Stell showed that one can determine the pair correlation function h(r) of the hard-sphere fluid for all distances r by specifying only the ``tail'' of the direct correlation function c(r) at separations greater than the hard-core diameter. We extend this idea in a very natural way to potentials with a soft repulsive core of finite extent and a weaker and longer ranged tail. We introduce a new continuous function T(r) which reduces exactly to the tail of c(r) outside the (soft) core region and show that both h(r) and c(r) depend only on the ``out projection'' of T(r): i.e., the product of the Boltzmann factor of the repulsive core potential times T(r). Standard integral equation closures can thus be reinterpreted and assessed in terms of their predictions for the tail of c(r) and simple approximations for its form suggest new closures. A new and very efficient variational method is proposed for solving the OrnsteinZernike equation given an approximation for the tail of c. Initial applications of these ideas to the Lennard-Jones and the hard-core Yukawa fluid are discussed. DOWNLOAD
[5]  Roles of repulsive and attractive forces in determining the structure of nonuniform liquids: Generalized mean field theory J. D. Weeks, K. Katsov, K. Vollmayr Phys. Rev. Lett., 81, 4400-4403 (1998). The structure of a nonuniform Lennard-Jones (LJ) liquid near a hard wall is approximated by that of a reference fluid with repulsive intermolecular forces in a self-consistently determined external mean field incorporating the effects of attractive forces. We calculate the reference fluid structure by first determining the response to the slowly varying part of the field alone, followed by the response to the harshly repulsive part. Both steps can be carried out very accurately, as confirmed by Monte Carlo simulations, and good agreement with the structure of the full LJ fluid is found. DOWNLOAD
[4]  Intermolecular forces and the structure of uniform and nonuniform fluids J. D. Weeks, K. Vollmayr, K. Katsov Physica A, 244, 461-475 (1997). Wc discuss the ramifications of Widom's idea that attractive intermolecular forces essentially cancel in dense uniform liquids. This idea was used directly in the WCA theory of uniform liquids, where the structure of the liquid is approximated by that of a simpler reference fluid with purely repulsive intermolecular forces. To take account of the unbalanced attractive forces found in nonuniform fluids, Weeks, Selinger, and Broughton (WSB) developed a new method where the structure is related to that of a nonuniform reference fluid in an external field chosen to yield a self-consistent description of correlations induced by the repulsive forces and a mean field treatment of the attractive forces. Using simulations, we provide a quantitative test of the accuracy of both methods for the uniform fluid at different points in the phase diagram by relating correlation functions in the uniform fluid to those in a nonuniform fluid with a particle fixed at the origin. We find that at high densities the WSB approach can correct most of the small errors in the structure of the WCA reference fluid. At lower densities the WSB method provides a considerable improvement over the WCA theory. A simplified version of the WSB method is presented that is of comparable accuracy. DOWNLOAD
[3]  Effective rotational Hamiltonians on the basis of classical representations: Rotational spectrum of the KCN molecule in the ground vibronic state S. V. Petrov, K. Katsov Opt. Spectrosc., 82, 361-364 (1997). The method for constructing the effective rotational Hamiltonian based on minimizing the classical Hamiltonian function, which was used earlier to obtain the rotational terms of diatomic molecules, is applied here to calculate the rotational levels of the ground vibronic state of the KCN molecule. The model with "frozen" lengths of the C-N and K-CN bonds adopted in this work allows the upper levels of rotational multiplets to be calculated with high accuracy. Calculations are carried out for J <= 4, and the accuracy increases with increasing J and is better than 0.04 for J = 4. LINK
[2]  A-priori effective rotational Hamiltonians - rotational spectra of some simple molecular models S. V. Petrov, K. Katsov Chem. Phys. Lett., 246, 646-653 (1995). A method proposed earlier [S.V, Petrov, Spcctry. Letters 26 (1993) 47; Prec. SPIE 2205 (1994) 173] for the study of the qualitative features of molecular re-vibrational dynamics is used for calculations of to-vibrational energies. As examples, the ro-vibrational levels of Na2 and KCN are calculated. DOWNLOAD
[1]  Effective rotational Hamiltonians within a classical approach - rotational terms of diatomic molecules S. V. Petrov, K. Katsov Opt. Spektrosk., 78, 738-741 (1995). A method for constructing the effective rotational Hamiltonian for an isolated vibrational state directly from the classical vibrational–rotational Hamilton function, without invoking the experimental data on rotational spectra, is suggested. Test calculations are carried out for diatomic molecules. The relative accuracy of the rotational-level calculations is on the order of 10^(–5). LINK
From unifrom to nonuniform liquids: A journey with density fluctuation theory K. Katsov Ph.D. Thesis, Chemical Physics, University of Maryland (2000). DOWNLOAD