Finite String Research Articles

Theoretical Investigation into Polymorphic Transformation between β-HMX and δ-HMX by Finite Temperature String

Polymorphic transformation is important in chemical industries, in particular, in those involving explosive molecular crystals. However, due to simulating challenges in the rare event method and collective variables, understanding the transformation mechanism of molecular crystals with a complex structure at the molecular level is poor. In this work, with the constructed order parameters (OPs) and K-means clustering algorithm, the potential of mean force (PMF) along the minimum free-energy path connecting β-HMX and δ-HMX was calculated by the finite temperature string method in the collective variables (SMCV), the free-energy profile and nucleation kinetics were obtained by Markovian milestoning with Voronoi tessellations, and the temperature effect on nucleation was also clarified. The barriers of transformation were affected by the finite-size effects. The configuration with the lower potential barrier in the PMF corresponded to the critical nucleus. The time and free-energy barrier of the polymorphic transformation were reduced as the temperature increased, which was explained by the pre-exponential factor and nucleation rate. Thus, the polymorphic transformation of HMX could be controlled by the temperatures, as is consistent with previous experimental results. Finally, the HMX polymorph dependency of the impact sensitivity was discussed. This work provides an effective way to reveal the polymorphic transformation of the molecular crystal with a cyclic molecular structure, and further to prepare the desired explosive by controlling the transformation temperature.

Uncloneable Quantum Advice

The famous no-cloning principle has been shown recently to enable a number of uncloneable cryptographic primitives, including the copy-protection of certain functionalities. Here we address for the first time unkeyed quantum uncloneablity, via the study of a complexity-theoretic tool that enables a computation, but that is natively unkeyed: quantum advice. Remarkably, this is an application of the no-cloning principle in a context where the quantum states of interest are not chosen by a random process. We establish unconditional constructions for promise problems admitting uncloneable quantum advice and, assuming the feasibility of quantum copy-protecting certain functions, for languages with uncloneable advice. Along the way, we note that state complexity classes, introduced by Rosenthal and Yuen (ITCS 2022) — which concern the computational difficulty of synthesizing sequences of quantum states — can be naturally generalized to obtain state cloning complexity classes. We make initial observations on these classes, notably obtaining a result analogous to the existence of undecidable problems. Our proof technique defines and constructs ingenerable sequences of finite bit strings, essentially meaning that they cannot be generated by any uniform circuit family with non-negligible probability. We then prove a generic result showing that the difficulty of accomplishing a computational task on uniformly random inputs implies its difficulty on any fixed, ingenerable sequence. We use this result to derandomize quantum cryptographic games that relate to cloning, and then incorporate a result of Kundu and Tan (arXiv 2022) to obtain uncloneable advice. Applying this two-step process to a monogamy-of-entanglement game yields a promise problem with uncloneable advice, and applying it to the quantum copy-protection of pseudorandom functions with super-logarithmic output lengths yields a language with uncloneable advice.

P-m-Mitotic Sets and Arithmetical Hierarchy

Let {0,1}∗be the set of all finite strings of elements from {0,1}, and let Pbe the class of problems recognized by deterministic Turing machines, which run in polynomial time (a problem is simply a subset of {0,1}∗). This article defines the class 𝐏(and shows that 𝐏(is isomorphic to the class 𝐏. Based on the notions of T-mitoticity and T-autoreducibility, K.Ambos-Spies introduced the notions of P-m-mitoticity and P-m-autoreducibility. The notions of P)-m-mitoticity and P)-m-autoreducibility are introduced by analogy with the mentioned notions.The article proves that the index sets {𝑧|𝑊"is P(-m-mitotic} and {z|𝑊"is P(-m-autoreducible} are Σ#-complete.

Finite Temperature String with Order Parameter as Collective Variables for Molecular Crystal: A Case of Polymorphic Transformation of TNT under External Electric Field.

An external electric field is an effective tool to induce the polymorphic transformation of molecular crystals, which is important practically in the chemical, material, and energy storage industries. However, the understanding of this mechanism is poor at the molecular level. In this work, two types of order parameters (OPs) were constructed for the molecular crystal based on the intermolecular distance, bond orientation, and molecular orientation. Using the K-means clustering algorithm for the sampling of OPs based on the Euclidean distance and density weight, the polymorphic transformation of TNT was investigated using a finite temperature string (FTS) under external electric fields. The potential of mean force (PMF) was obtained, and the essence of the polymorphic transformation between o-TNT and m-TNT was revealed, which verified the effectiveness of the FTS method based on K-means clustering to OPs. The differences in PMFs between the o-TNT and transition state were decreased under external electric fields in comparison with those in no field. The fields parallel to the c-axis obviously affected the difference in PMF, and the relationship between the changes in PMFs and field strengths was found. Although the external electric field did not promote the convergence, the time of the polymorphic transformation was reduced under the external electric field in comparison to its absence. Moreover, under the external electric field, the polymorphic transformation from o-TNT to m-TNT occurred while that from m-TNT to o-TNT was prevented, which was explained by the dipole moment of molecule, relative permittivity, chemical potential difference, nucleation work and nucleation rate. This confirmed that the polymorphic transformation orientation of the molecular crystal could be controlled by the external electric field. This work provides an effective way to explore the polymorphic transformation of the molecular crystals at a molecular level, and it is useful to control the production process and improve the performance of energetic materials by using the external electric fields.

Thermodynamics of Computations with Absolute Irreversibility, Unidirectional Transitions, and Stochastic Computation Times

Developing a thermodynamic theory of computation is a challenging task at the interface of nonequilibrium thermodynamics and computer science. In particular, this task requires dealing with difficulties such as stochastic halting times, unidirectional (possibly deterministic) transitions, and restricted initial conditions, features common in real-world computers. Here, we present a framework which tackles all such difficulties by extending the martingale theory of nonequilibrium thermodynamics to generic nonstationary Markovian processes, including those with broken detailed balance and/or absolute irreversibility. We derive several universal fluctuation relations and second-law-like inequalities that provide both lower and upper bounds on the intrinsic dissipation (mismatch cost) associated with any periodic process—in particular, the periodic processes underlying all current digital computation. Crucially, these bounds apply even if the process has stochastic stopping times, as it does in many computational machines. We illustrate our results with exhaustive numerical simulations of deterministic finite automata processing bit strings, one of the fundamental models of computation from theoretical computer science. We also provide universal equalities and inequalities for the acceptance probability of words of a given length by a deterministic finite automaton in terms of thermodynamic quantities, and outline connections between computer science and stochastic resetting. Our results, while motivated from the computational context, are applicable far more broadly. Published by the American Physical Society 2024

A weak theory of building blocks

AbstractWe apply the mereological concept of parthood to the coding of finite sequences. We propose a first‐order theory in which coding finite sequences is intuitive and transparent. We compare this theory with Robinson arithmetic, adjunctive set theory and weak theories of finite strings and finite trees using interpretability.

Gluon scattering in AdS at finite string coupling from localization

We consider gluons scattering in Type IIB string theory on AdS5 × S5/ℤ2 in the presence of D7 branes, which is dual to the flavor multiplet correlator in a certain 4d N\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ \\mathcal{N} $$\\end{document} = 2 USp(2N) gauge theory with SO(8) flavor symmetry and complexified coupling τ. We compute this holographic correlator in the large N and finite τ expansion using constraints from derivatives of the mass deformed sphere free energy, which we compute to all orders in 1/N and finite τ using supersymmetric localization. In particular, we fix the F4 higher derivative correction to gluon scattering on AdS at finite string coupling τs = τ in terms of Jacobi theta functions, which feature the expected relations between the SL(2, ℤ) duality and the SO(8) triality of the CFT, and match it to the known flat space term. We also use the flat space limit to compute D2F4 corrections of the correlator at finite τ in terms of a non-holomorphic Eisenstein series. At weak string coupling, we find that the AdS correlator takes a form which is remarkably similar to that of the flat space Veneziano amplitude.

Passive-guaranteed modeling and simulation of a finite element nonlinear string model

This paper proposes to solve the dynamics of the Kirchhoff-Carrier nonlinear string model using the finite elements method. In order to ensure the power balance of the resulting finite dimensional model it is rewritten in the Port-Hamiltonian System (PHS) formalism. Using a discrete gradient and a quadratization of the Hamiltonian, an explicit power-preserving numerical scheme is proposed. Results of simulation are presented.

Finite temperature string by K-means clustering sampling with order parameters as collective variables for molecular crystals: application to polymorphic transformation between β-CL-20 and ε-CL-20.

Polymorphic transformation of molecular crystals is a fundamental phase transition process, and it is important practically in the chemical, material, biopharmaceutical, and energy storage industries. However, understanding of the transformation mechanism at the molecular level is poor due to the extreme simulating challenges in enhanced sampling and formulating order parameters (OPs) as the collective variables that can distinguish polymorphs with quite similar and complicated structures so as to describe the reaction coordinate. In this work, two kinds of OPs for CL-20 were constructed by the bond distances, bond orientations and relative orientations. A K-means clustering algorithm based on the Euclidean distance and sample weight was used to smooth the initial finite temperature string (FTS), and the minimum free energy path connecting β-CL-20 and ε-CL-20 was sketched by the string method in collective variables, and the free energy profile along the path and the nucleation kinetics were obtained by Markovian milestoning with Voronoi tessellations. In comparison with the average-based sampling, the K-means clustering algorithm provided an improved convergence rate of FTS. The simulation of transformation was independent of OP types but was affected greatly by finite-size effects. A surface-mediated local nucleation mechanism was confirmed and the configuration located at the shoulder of potential of mean force, rather than overall maximum, was confirmed to be the critical nucleus formed by the cooperative effect of the intermolecular interactions. This work provides an effective way to explore the polymorphic transformation of caged molecular crystals at the molecular level.

Understanding the open string pair production of the Dp/D0 system

Consider a system consisting of Dp and Dp′, placed parallel at a separation and with p − p′ = 2n (assuming p ≥ p′, the integer n ≥ 0 and p′ > 0). When either Dp or Dp′ carries a worldvolume electric flux, one in general expects a non-vanishing open string pair production due to the pair of virtual open string/anti open string connecting the two D branes under the action of the applied flux. However, this will not be true for p′ = 0 and p = 2, 4, 6 when the Dp carries a pure electric flux. In this note, we will explore the case for which a finite non-vanishing open string pair production rate can indeed be produced when a certain worldvolume flux is applied to the Dp brane and understand the physics behind.

Generalized initial-boundary problem for the wave equation with mixed derivative

We study an initial-boundary problem for a second-order inhomogeneous hyperbolic equation in a half-strip of the plane containing a mixed derivative with constant coefficients and zero or nonzero potential. This equation is the equation of transverse oscillations of a moving finite string. The case of zero initial velocity and fixed ends (Dirichlet conditions) is considered. It is assumed that the roots of the characteristic equation are simple and lie on the real axis on opposite sides of the origin. The classical solution of the initial-boundary problem is determined. In the case of zero potential, a uniqueness theorem for the classical solution is formulated and a formula for the solution is given in the form of a series consisting of contour integrals containing the initial data of the problem. Based on this formula, the concepts of a generalized initial-boundary value problem and a generalized solution are introduced. The main theorems on finite formulas for the generalized solution in the case of homogeneous and inhomogeneous problems are formulated. To prove these theorems, we apply an approach that uses the theory of divergent series in the sense of Euler, proposed by A.P. Khromov (axiomatic approach). Using this approach, on the basis of formulas for solutions in the form of a series, the formulated main theorems are proved. Further, as an application of the main theorems obtained, we prove a theorem on the existence and uniqueness of a generalized solution of the initial-boundary problem in the presence of a nonzero summable potential and give a formula for the solution in the form of an exponentially convergent series.

The category of finite strings

The category of finite strings

Reconstruction of Two Functions in the Model of Vibrations of a String One End of Which Is Placed in a Moving Medium

The paper considers an inverse problem of determining the coefficients in the model of small transverse vibrations of a homogeneous finite string one end of which is placed in a moving medium and the other is free. The vibrations are simulated by a hyperbolic equation on an interval. One boundary condition has a nonclassical form. Additional data for solving the inverse problem are the values of the solution of the forward problem with a known fixed value of the spatial argument. In the inverse problem, it is required to determine the function in the nonclassical boundary condition and a functional factor on the right-hand side of the equation. Uniqueness and existence theorems for the inverse problem are proved. For the forward problem, conditions for unique solvability are established in a form that simplifies the analysis of the inverse problem. For the numerical solution of the inverse problem, an algorithm is proposed for the stage-by-stage separate reconstruction of the sought-for functions using the method of successive approximations for integral equations.

Transition Path Theory for Langevin Dynamics on Manifolds: Optimal Control and Data-Driven Solver

We present a data-driven point of view for rare events, which represent conformational transitions in biochemical reactions modeled by overdamped Langevin dynamics on manifolds in high dimensions. We first reinterpret the transition state theory and the transition path theory from the optimal control viewpoint. Given a point cloud probing the manifold, we construct a discrete Markov chain with a -matrix computed from an approximated Voronoi tesselation via the point cloud. We use this -matrix to compute a discrete committor function whose level set automatically orders the point cloud. Then based on the committor function, an optimally controlled random walk on point clouds is constructed and utilized to efficiently sample transition paths, which become an almost sure event in time instead of a rare event in the original reaction dynamics. To compute the mean transition path efficiently, a local averaging algorithm based on the optimally controlled random walk is developed, which adapts the finite temperature string method to the controlled Monte Carlo samples. Numerical examples on sphere/torus including a conformational transition for the alanine dipeptide in vacuum are conducted to illustrate the data-driven solver for the transition path theory on point clouds. The mean transition path obtained via the controlled Monte Carlo simulations highly coincides with the computed dominant transition path in the transition path theory.

On the Countering of Free Vibrations by Forcing: Part II—Damped Oscillations and Decaying Forcing

The present two-part paper concerns the active vibration suppression for the simplest damped continuous system, namely the transverse oscillations of an elastic string, with constant tension and mass density per unit length and friction force proportional to the velocity, described by the telegraph or wave-diffusion equation, in two complementary parts. The initial part I considers non-resonant and resonant forcing, by concentrated point forces or continuous force distributions independent of time, with phase shift between the forced and free oscillations, in the absence of damping, in which case the forced telegraph equation reduces to the forced classical wave equation. The present and final part II uses the forced wave-diffusion equation to model the effect of damping, both as amplitude decay and phase shift in time, for non-resonant and resonant forcing by a single point force, with constant magnitude or magnitude decaying exponentially in time at an arbitrary rate. Assuming a finite elastic string fixed at both ends, the free oscillations are (i) sinusoidal modes in space-time with exponential decay in time due to damping. The non-resonant forced oscillations at an applied frequency distinct from a natural frequency are also (ii) sinusoidal in space-time, with constant amplitude and a phase shift such that the work of the applied force balances the dissipation. For resonant forcing at an applied frequency equal to a natural frequency, the sinusoidal oscillations in space-time have (iii) a constant amplitude and a phase shift of π/2. In both cases, the (ii) non-resonant or (iii) resonant forcing dominates the decaying free oscillations after some time. Even by optimizing the forcing to minimize the total energy of oscillation, it remains below the energy of the free oscillation alone, but only for a short time—generally a fraction of the period. A more effective method of countering the damped free oscillations is to use forcing with amplitude decaying exponentially in time; by suitable choice of the forcing decay relative to the free damping, the total energy of oscillation over all time can be reduced to no more than 1/16th of the energy of the free oscillation.

Transition state searching for complex biomolecules: Algorithms and machine learning

Transition state is a key concept for chemists to understand and fine-tune the conformational changes of large biomolecules. Due to its short residence time, it is difficult to capture a transition state via experimental techniques. Characterizing transition states for a conformational change therefore is only achievable via physics-driven molecular dynamics simulations. However, unlike chemical reactions which involve only a small number of atoms, conformational changes of biomolecules depend on numerous atoms and therefore the number of their coordinates in our 3D space. The searching for their transition states will inevitably encounter the curse of dimensionality, i.e. the reaction coordinate problem, which invokes the invention of various algorithms for solution. Recent years, new machine learning techniques and the incorporation of some of them into the transition state searching methods emerged. Here, we first review the design principle of representative transition state searching algorithms, including the collective-variable (CV)-dependent gentlest ascent dynamics, finite temperature string, fast tomographic, travelling-salesman based automated path searching, and the CV-independent transition path sampling. Then, we focus on the new version of TPS that incorporates reinforcement learning for efficient sampling, and we also clarify the suitable situation for its application. Finally, we propose a new paradigm for transition state searching, a new dimensionality reduction technique that preserves transition state information and combines gentlest ascent dynamics.

The Point of No Return: Evolution of Excess Mutation Rate Is Possible Even for Simple Mutation Models

Under constant selection, each trait has a fixed fitness, and small mutation rates allow populations to efficiently exploit the optimal trait. Therefore, it is reasonable to expect that mutation rates will evolve downwards. However, we find that this need not be the case, examining several models of mutation. While upwards evolution of the mutation rate has been found with frequency- or time-dependent fitness, we demonstrate its possibility in a much simpler context. This work uses adaptive dynamics to study the evolution of the mutation rate, and the replicator–mutator equation to model trait evolution. Our approach differs from previous studies by considering a wide variety of methods to represent mutation. We use a finite string approach inspired by genetics as well as a model of local mutation on a discretization of the unit intervals, handling mutation beyond the endpoints in three ways. The main contribution of this work is a demonstration that the evolution of the mutation rate can be significantly more complicated than what is usually expected in relatively simple models.

Time-varying spectrum of the random string* *It is a pleasure to dedicate this paper to Prof. Igor Jex, who has made fundamental contributions to quantum dynamics and the interface with classical mechanics. In that spirit, this paper extends the results of van Lear Jr and Uhlenbeck on the random string to the nonstationary case using the Wigner distribution.

We consider the response of a finite string to white noise and obtain the exact time-dependent spectrum. The complete exact solution is obtained, that is, both the transient and steady-state solution. To define the time-varying spectrum we ensemble average the Wigner distribution. We obtain the exact solution by transforming the differential equation for the string into the phase space differential equation of time and frequency and solve it directly. We also obtain the exact solution by an impulse response method which gives a different form of the solution. Also, we obtain the time-dependent variance of the process at each position. Limiting cases for small and large times are obtained. As a special case we obtain the results of van Lear Jr and Uhlenbeck and Lyon. A numerical example is given and the results plotted.

Sequential Measurements, Topological Quantum Field Theories, and Topological Quantum Neural Networks

AbstractWe introduce novel methods for implementing generic quantum information within a scale‐free architecture. For a given observable system, we show how observational outcomes are taken to be finite bit strings induced by measurement operators derived from a holographic screen bounding the system. In this framework, measurements of identified systems with respect to defined reference frames are represented by semantically‐regulated information flows through distributed systems of finite sets of binary‐valued Barwise‐Seligman classifiers. Specifically, we construct a functor from the category of cone‐cocone diagrams (CCCDs) over finite sets of classifiers, to the category of finite cobordisms of Hilbert spaces. We show that finite CCCDs provide a generic representation of finite quantum reference frames (QRFs). Hence the constructed functor shows how sequential finite measurements can induce TQFTs. The only requirement is that each measurement in a sequence, by itself, satisfies Bayesian coherence, hence that the probabilities it assigns satisfy the Kolmogorov axioms. We extend the analysis too develop topological quantum neural networks (TQNNs), which enable machine learning with functorial evolution of quantum neural 2‐complexes (TQN2Cs) governed by TQFTs amplitudes, and resort to the Atiyah‐Singer theorems in order to classify topological data processed by TQN2Cs. We then comment about the quiver representation of CCCDs and generalized spin‐networks, a basis of the Hilbert spaces of both TQNNs and TQFTs. We finally review potential implementations of this framework in solid state physics and suggest applications to quantum simulation and biological information processing.

String C-groups with real Schur index 2

We give examples of finite string C -groups (the automorphism groups of abstract regular polytopes) that have irreducible characters of real Schur index 2. This answers a problem of Monson concerning these groups.