A long and narrow channel confines disks of two sizes. The disks are randomly agitated in a widened channel under moderate pressure, then jammed according to a tunable protocol. We present exact results that characterize jammed macrostates (volume, entropy, jamming patterns). The analysis divides jammed disk sequences into overlapping tiles out of which statistically interacting quasiparticles are constructed. The fractions of small and large disks are controlled by a chemical potential adapted to configurational statistics of granular matter. The results show regimes for the energy parameters (determined by the jamming protocol) that either enhance or suppress the mixing of disk sizes. Size segregation or size alternation driven by steric forces alone are manifestations of a broken symmetry.

Disks of two sizes are confined to a long and narrow channel. The axis and the plane of the channel are horizontal. The channel is closed off by pistons that freeze jammed microstates out of loose disk configurations, agitated randomly at calibrated intensity and subject to moderate pressure. Disk sizes and channel width are such that under jamming no disks remain loose and all disks touch one wall. The protocol permits disks to move past each other prior to jamming, which facilitates randomness in the sequence of large and small disks. We present exact results for the characterization of jammed macrostates including volume and entropy for given fractions of small and large disks as functions of energy parameters which depend on the jamming protocol. Our analysis divides the disk sequence of jammed microstates into overlapping tiles out of which we construct 17 species of statistically interacting quasiparticles. Jammed macrostates then depend on the fractions of small and large disks and on a dimensionless control parameter inferred from measures for expansion work against the pistons and intensity of random agitations. Two models are introduced for comparison of key technical aspects: one model emphasizes symmetry and the other mechanical stability. We distinguish regimes for the energy parameters that either enhance or suppress mixing of disk sizes in jammed macrostates. The latter case, if realizable, is a manifestation of grain segregation driven by steric forces alone, without directional bias.

The work teaches all the basic mathematical methods and tools needed by the physicist, both in graduate study and in practice. The methods are presented compactly and with consistent notation, and the author uses explanatory color graphics and tasks with solutions to explain the material in a clear and easy-to-understand manner.

A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination of tension and torque involves, in the framework of this method of analysis, the (thermal or mechanical) activation of a specific mix of statistically interacting particles carrying quanta of extension or contraction and quanta of twist or supercoiling. The methodology, which is elucidated in applications of increasing complexity, is capable of describing the conversion between twist chirality and plectonemic chirality in quasistatic processes. The control variables are force or extension and torque or linkage (a combination of twist and writhe). The versatility of this approach is demonstrated in two applications relevant and promising for double-stranded DNA under controlled tension and torque. One application describes conformational transformations between (native) B-DNA, (underwound) S-DNA, and (overwound) P-DNA in accord with experimental data. The other application describes how the conversion between a twisted chain and a supercoiled chain accommodates variations of linkage and excess length in a buckling transition.

Free-energy landscapes for short peptides-specifically for variants of the pH low insertion peptide (pHLIP)-in the heterogeneous environment of a lipid bilayer or cell membrane are constructed, taking into account a set of dominant interactions and the conformational preferences of the peptide backbone. Our methodology interprets broken internal H-bonds along the backbone of a polypeptide as statistically interacting quasiparticles, activated from the helix reference state. The favored conformation depends on the local environment (ranging from polar to nonpolar), specifically on the availability of external H-bonds (with H_{2}O molecules or lipid headgroups) to replace internal H-bonds. The dominant side-chain contribution is accounted for by residue-specific transfer free energies between polar and nonpolar environments. The free-energy landscape is sensitive to the level of pH in the aqueous environment surrounding the membrane. For high pH, we identify pathways of descending free energy that suggest a coexistence of membrane-adsorbed peptides with peptides in solution. A drop in pH raises the degree of protonation of negatively charged residues and thus increases the hydrophobicity of peptide segments near the C terminus. For low pH, we identify insertion pathways between the membrane-adsorbed state and a stable trans-membrane state with the C terminus having crossed the membrane.

This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds between monomers or of entire groups of monomers to tension is governed by the activation of statistically interacting particles representing quanta of extension or contraction. This method of analysis is capable of describing thermal unbending of the freely jointed or wormlike chain kind, linear or nonlinear contour elasticity, and structural transformations including effects of cooperativity. The versatility of this approach is demonstrated in an application to double-stranded DNA undergoing torsionally unconstrained stretching across three regimes of mechanical response including an overstretching transition. The three-regime force-extension characteristic, derived from a single free-energy expression, accurately matches empirical evidence.

We consider a lattice gas in spaces of dimensionality D=1,2,3. The particles are subject to a hardcore exclusion interaction and an attractive pair interaction that satisfies Gauss' law as do Newtonian gravity in D=3, a logarithmic potential in D=2, and a distance-independent force in D=1. Under mild additional assumptions regarding symmetry and fluctuations we investigate equilibrium states of self-gravitating material clusters, in particular radial density profiles for closed and open systems. We present exact analytic results in several instances and high-precision numerical data in others. The density profile of a cluster with finite mass is found to exhibit exponential decay in D=1 and power-law decay in D=2 with temperature-dependent exponents in both cases. In D=2 the gas evaporates in a continuous transition at a nonzero critical temperature. We describe clusters of infinite mass in D=3 with a density profile consisting of three layers (core, shell, halo) and an algebraic large-distance asymptotic decay. In D=3 a cluster of finite mass can be stabilized at T>0 via confinement to a sphere of finite radius. In some parameter regime, the gas thus enclosed undergoes a discontinuous transition between distinct density profiles. For the free energy needed to identify the equilibrium state we introduce a construction of gravitational self-energy that works in all D for the lattice gas. The decay rate of the density profile of an open cluster is shown to transform via a stretched exponential for 1<D<2, whereas it crosses over from one power-law at intermediate distances to a different power-law at larger distances for 2<D<3.

We propose a method for calculating dynamical correlation functions at finite temperature in integrable lattice models of Yang-Baxter type. The method is based on an expansion of the correlation functions as a series over matrix elements of a time-dependent quantum transfer matrix rather than the Hamiltonian. In the infinite Trotter-number limit the matrix elements become time independent and turn into the thermal form factors studied previously in the context of static correlation functions. We make this explicit with the example of the XXZ model. We show how the form factors can be summed utilizing certain auxiliary functions solving finite sets of nonlinear integral equations. The case of the XX model is worked out in more detail leading to a novel form-factor series representation of the dynamical transverse two-point function.

We present the exact solution of a microscopic statistical mechanical model for the transformation of a long polypeptide between an unstructured coil conformation and an α-helix conformation. The polypeptide is assumed to be adsorbed to the interface between a polar and a non-polar environment such as realized by water and the lipid bilayer of a membrane. The interfacial coil-helix transformation is the first stage in the folding process of helical membrane proteins. Depending on the values of model parameters, the conformation changes as a crossover, a discontinuous transition, or a continuous transition with helicity in the role of order parameter. Our model is constructed as a system of statistically interacting quasiparticles that are activated from the helix pseudo-vacuum. The particles represent links between adjacent residues in coil conformation that form a self-avoiding random walk in two dimensions. Explicit results are presented for helicity, entropy, heat capacity, and the average numbers and sizes of sboth coil and helix segments.

We consider linear arrays of cells of volume V(c) populated by monodisperse rods of size σV(c),σ=1,2,..., subject to hardcore exclusion interaction. Each rod experiences a position-dependent external potential. In one application we also examine effects of contact forces between rods. We employ two distinct methods of exact analysis with complementary strengths and different limits of spatial resolution to calculate profiles of pressure and density on mesoscopic and microscopic length scales at thermal equilibrium. One method uses density functionals and the other statistically interacting vacancy particles. The applications worked out include gravity, power-law traps, and hard walls. We identify oscillations in the profiles on a microscopic length scale and show how they are systematically averaged out on a well-defined mesoscopic length scale to establish full consistency between the two approaches. The continuum limit, realized as V(c)→0,σ→∞ at nonzero and finite σV(c), connects our highest-resolution results with known exact results for monodisperse rods in a continuum. We also compare the pressure profiles obtained from density functionals with the average microscopic pressure profiles derived from the pair distribution function.

This work investigates jammed granular matter under conditions that produce heterogeneous mass distributions on a mesoscopic scale. We consider a system of identical disks that are confined to a narrow channel, open at one end and closed off at the other end. The disks are jammed by the local pressure in a gravitational field or centrifuge. All surfaces are hard and frictionless. We calculate the profiles of pressure, mass density, and entropy density on a mesoscopic length scale under the assumption that the jammed states are produced by random agitations of uniform intensity along the channel. These profiles exhibit trends and features governed by the balancing of position-dependent forces and potential energies. The analysis employs a method of configurational statistics that uses interlinking two-disk tiles as the fundamental degrees of freedom. Configurational statistics weighs the probabilities of tiles according to competing potential energies associated with gravity and centrifugation. Amendments account for the effects of the marginal stability of some tiles due to competing forces.

The equilibrium statistical mechanics of one-dimensional lattice gases with interactions of arbitrary range and shape between first-neighbor atoms is solved exactly on the basis of statistically interacting vacancy particles. Two sets of vacancy particles are considered. In one set all vacancies are of one-cell size. In the other set the sizes of vacancy particles match the separation between atoms. Explicit expressions are obtained for the Gibbs free energy and the distribution of spaces between atoms at thermal equilibrium. Applications to various types of interaction potentials are discussed, including long-range potentials that give rise to phase transitions. Extensions to hard rod systems are straightforward and are shown to agree with existing results for lattice models and their continuum limits.

A system of identical disks is confined to a narrow channel, closed off at one end by a stopper and at the other end by a piston. All surfaces are hard and frictionless. A uniform gravitational field is directed parallel to the plane of the disks and perpendicular to the axis of the channel. We employ a method of configurational statistics that interprets jammed states as configurations of floating particles with structure. The particles interlink according to set rules. The two jammed microstates with smallest volume act as a pseudo-vacuum. The placement of particles is subject to a generalized Pauli principle. Jammed macrostates are generated by random agitations and specified by two control variables. They are inferred from measures for expansion work against the piston, gravitational potential energy, and intensity of random agitations. In this two-dimensional space of variables there exists a critical point. The jammed macrostate realized at the critical point depends on the path of approach. We describe all jammed macrostates by volume and entropy. Both are functions of the average population densities of particles. Approaching the critical point in an extended space of control variables generates two types of jammed macrostates: states with random heterogeneities in mass density and states with domains of uniform mass density. Criticality is shown to be robust against some effects of friction.

The s = 1/2 Ising chain with uniform nearest-neighbor and next-nearest-neighbor coupling is used to construct a system of floating particles characterized by motifs of up to six consecutive local spins.The spin couplings cause the assembly of particles which, in turn, remain free of interaction energies even at high density.All microstates are configurations of particles from one of three different sets, excited from pseudo-vacua associated with ground states of periodicities one, two, and four.The motifs of particles and elements of pseudo-vacuum interlink in two shared site variables.The statistical interaction between particles is encoded in a generalized Pauli principle, describing how the placement of one particle modifies the options for placing further particles.In the statistical mechanical analysis arbitrary energies can be assigned to all particle species.The entropy is a function of the particle populations.The statistical interaction specifications are transparently built into that expression.The energies and structures of the particles alone govern the ordering at low temperature.Under special circumstances the particles can be replaced by more fundamental particles with shorter motifs that interlink in only one shared site variable.Structures emerge from interactions on two levels: particles with shapes from coupled spins and long-range ordering tendencies from statistically interacting particles with shapes.

The s=3/2 Ising spin chain with uniform nearest-neighbor coupling, quadratic single-site potential, and magnetic field is shown to be equivalent to a system of 17 species of particles with internal structure. The same set of particles (with different energies) is shown to generate the spectrum of the s=1/2 Ising chain with dimerized nearest-neighbor coupling. The particles are free of interaction energies even at high densities. The mutual exclusion statistics of particles from all species is determined by their internal structure and encoded in a generalized Pauli principle. The exact statistical mechanical analysis can be performed for thermodynamically open or closed systems and with arbitrary energies assigned to all particle species. Special circumstances make it possible to merge two or more species into a single species. All traits that distinguish the original species become ignorable. The particles from the merged species are effectively indistinguishable and obey modified exclusion statistics. Different mergers may yield the same end product, implying that the inverse process (splitting any species into subspecies) is not unique. In a macroscopic system of two merged species at thermal equilibrium, the concentrations of the original species satisfy a functional relation governed by their mutual statistical interaction. That relation is derivable from an extremum principle. In the Ising context the system is open and the particle energies depend on the Hamiltonian parameters. Simple models of polymerization and solitonic paramagnetism each represent a closed system of two species that can transform into each other. Here they represent distinguishable traits with different energies of the same physical particle.

We analyze the absorption of microwaves by the Heisenberg-Ising chain combining exact calculations, based on the integrability of the model, with numerical calculations. Within linear response theory, the absorbed intensity is determined by the imaginary part of the dynamical susceptibility. The moments of the normalized intensity can be used to define the shift of the resonance frequency induced by the interactions and the linewidth independently of the shape of the spectral line. These moments can be calculated exactly as functions of temperature and strength of an external magnetic field, as long as the field is directed along the symmetry axis of the chain. This allows us to discuss the linewidth and the resonance shift for a given magnetic field in the full range of possible anisotropy parameters. For the interpretation of these data, we need a qualitative knowledge of the line shape, which we obtain from fully numerical calculations for finite chains. Exact analytical results on the line shape are out of reach of current theories. From our numerical work, we could extract, however, an empirical parameter-free model of the line shape at high temperatures, which is extremely accurate over a wide range of anisotropy parameters, and is exact at the free-fermion and isotropic points. Another prediction of the line shape can be made in the zero-temperature and zero magnetic field limits, where the sufficiently anisotropic model shows strong absorption. For anisotropy parameters in the massive phase, we derive the exact two-spinon contribution to the spectral line. From the intensity sum rule, it can be estimated that this contribution accounts for more than 80$%$ of the spectral weight if the anisotropy parameter is moderately above its value at the isotropic point.

We analyze the absorption of microwaves by the Heisenberg-Ising chain combining exact calculations, based on the integrability of the model, with numerical calculations. Within linear response theory the absorbed intensity is determined by the imaginary part of the dynamical susceptibility. The moments of the normalized intensity can be used to define the shift of the resonance frequency induced by the interactions and the line width independently of the shape of the spectral line. These moments can be calculated exactly as functions of temperature and strength of an external magnetic field, as long as the field is directed along the symmetry axis of the chain. This allows us to discuss the line width and the resonance shift for a given magnetic field in the full range of possible anisotropy parameters. For the interpretation of these data we need a qualitative knowledge of the line shape which we obtain from fully numerical calculations for finite chains. Exact analytical results on the line shape are out of reach of current theories. From our numerical work we could extract, however, an empirical parameter-free model of the line shape at high temperatures which is extremely accurate over a wide range of anisotropy parameters and is exact at the free fermion point and at the isotropic point. Another prediction of the line shape can be made in the zero-temperature and zero magnetic field limit, where the sufficiently anisotropic model shows strong absorption. For anisotropy parameters in the massive phase we derive the exact two-spinon contribution to the spectral line. From the intensity sum rule it can be estimated that this contribution accounts for more than 80% of the spectral weight if the anisotropy parameter is moderately above its value at the isotropic point.