arXiv subjects

Yi-Hsuan Lin

Publications and source records attributed to Yi-Hsuan Lin.

At least 55 records · Page 3Linked to original sources

arXiv2022

Community Engagement Frontier

This is the summary report of the Community Engagement Frontier for the Snowmass 2021 study of the future of particle physics. The report discusses a number of general issues of importance to the particle physics community, including (1) the relation of universities, national laboratories, and industry, (2) career paths for scientists engaged in particle physics, (3) diversity, equity, and inclusion, (4) physics education, (5) public education and outreach, (6) engagement with the government and public policy, and (7) the environmental and social impacts of particle physics.

physics.soc-ph↗

arXiv2022

The Calderón problem for a nonlocal diffusion equation with time-dependent coefficients

We investigate global uniqueness for an inverse problem for a nonlocal diffusion equation on domains that are bounded in one direction. The coefficients are assumed to be unknown and isotropic on the entire space. We first show that the partial exterior Dirichlet-to-Neumann map locally determines the diffusion coefficient in the exterior domain. In addition, we introduce a novel analysis of nonlocal Neumann derivatives to prove an interior determination result. Interior and exterior determination yield the desired global uniqueness theorem for the Calderón problem of nonlocal diffusion equations with time-dependent coefficients. This work extends recent studies from nonlocal elliptic equations with global coefficients to their parabolic counterparts. The results hold for any spatial dimension $n\geq 1$.

math.AP↗

arXiv2022

Numerical Techniques for Applications of Analytical Theories to Sequence-Dependent Phase Separations of Intrinsically Disordered Proteins

Biomolecular condensates, physically underpinned to a significant extent by liquid-liquid phase separation (LLPS), are now widely recognized by numerous experimental studies to be of fundamental biological, biomedical, and biophysical importance. In the face of experimental discoveries, analytical formulations emerged as a powerful yet tractable tool in recent theoretical investigations of the role of LLPS in the assembly and dissociation of these condensates. The pertinent LLPS often involves, though not exclusively, intrinsically disordered proteins engaging in multivalent interactions that are governed by their amino acid sequences. For researchers interested in applying these theoretical methods, here we provide a practical guide to a set of computational techniques devised for extracting sequence-dependent LLPS properties from analytical formulations. The numerical procedures covered include those for the determinination of spinodal and binodal phase boundaries from a general free energy function with examples based on the random phase approximation in polymer theory, construction of tie lines for multiple-component LLPS, and field-theoretic simulation of multiple-chain heteropolymeric systems using complex Langevin dynamics. Since a more accurate physical picture often requires comparing analytical theory against explicit-chain model predictions, a commonly utilized methodology for coarse-grained molecular dynamics simulations of sequence-specific LLPS is also briefly outlined.

q-bio.BM↗

arXiv2022

Inverse problems for fractional equations with a minimal number of measurements

In this paper, we study several inverse problems associated with a fractional differential equation of the following form: \[ (-Δ)^s u(x)+\sum_{k=0}^N a^{(k)}(x) [u(x)]^k=0,\ \ 0<s<1,\ N\in\mathbb{N}\cup\{0\}\cup\{\infty\}, \] which is given in a bounded domain $Ω\subset\mathbb{R}^n$, $n\geq 1$. For any finite $N$, we show that $a^{(k)}(x)$, $k=0,1,\ldots, N$, can be uniquely determined by $N+1$ different pairs of Cauchy data in $Ω_e:=\mathbb{R}^n\backslash\overlineΩ$. If $N=\infty$, the uniqueness result is established by using infinitely many pairs of Cauchy data. The results are highly intriguing in that it generally does not hold true in the local case, namely $s=1$, even for the simplest case when $N=0$, a fortiori $N\geq 1$. The nonlocality plays a key role in establishing the uniqueness result. We also establish several other unique determination results by making use of a minimal number of measurements. Moreover, in the process we derive a novel comparison principle for nonlinear fractional differential equations as a significant byproduct.

math.AP↗

arXiv2021

An inverse problem for a semilinear elliptic equation on conformally transversally anisotropic manifolds

Given a conformally transversally anisotropic manifold $(M,g)$, we consider the semilinear elliptic equation $$(-Δ_{g}+V)u+qu^2=0\quad \text{on $M$}.$$ We show that an a priori unknown smooth function $q$ can be uniquely determined from the knowledge of the Dirichlet-to-Neumann map associated to the semilinear elliptic equation. This extends the previously known results of the works [FO20, LLLS21a]. Our proof is based on analyzing higher order linearizations of the semilinear equation with non-vanishing boundary traces and also the study of interactions of two or more products of the so-called Gaussian quasimode solutions to the linearized equation.

math.AP↗

arXiv2021

Simultaneous recoveries for semilinear parabolic systems

In this paper, we study inverse boundary problems associated with semilinear parabolic systems in several scenarios where both the nonlinearities and the initial data can be unknown. We establish several simultaneous recovery results showing that the passive or active boundary Dirichlet-to-Neumann operators can uniquely recover both of the unknowns, even stably in a certain case. It turns out that the nonlinearities play a critical role in deriving these recovery results. If the nonlinear term belongs to a general $C^1$ class but fulfilling a certain growth condition, the recovery results are established by the control approach via Carleman estimates. If the nonlinear term belongs to an analytic class, the recovery results are established through successive linearization in combination with special CGO (Complex Geometrical Optics) solutions for the parabolic system.

math.AP↗

arXiv2021

Assembly of Model Postsynaptic Densities Involves Interactions Auxiliary to Stoichiometric Binding

The assembly of functional biomolecular condensates often involves liquid-liquid phase separation (LLPS) of proteins with multiple modular domains, which can be folded or conformationally disordered to various degrees. To understand the LLPS-driving domain-domain interactions, a fundamental question is how readily the interactions in the condensed phase can be inferred from inter-domain interactions in dilute solutions. In particular, are the interactions leading to LLPS exclusively those underlying the formation of discrete inter-domain complexes in homogeneous solutions? We address this question by developing a mean-field LLPS theory of two stoichiometrically constrained solute species. The theory is applied to the neuronal proteins SynGAP and PSD-95, whose complex coacervate serves as a rudimentary model for neuronal postsynaptic densities (PSDs). The predicted phase behaviors are compared with experiments. Previously, a three-SynGAP, two-PSD-95 ratio was determined for SynGAP/PSD-95 complexes in dilute solutions. However, when this 3:2 stoichiometry is uniformly imposed in our theory encompassing both dilute and condensed phases, the tie-line pattern of the predicted SynGAP/PSD-95 phase diagram differs drastically from that obtained experimentally. In contrast, theories embodying alternate scenarios postulating auxiliary SynGAP-PSD-95 as well as SynGAP-SynGAP and PSD-95-PSD-95 interactions in addition to those responsible for stoichiometric SynGAP/PSD-95 complexes produce tie-line patterns consistent with experiment. Hence, our combined theoretical-experimental analysis indicates that weaker interactions or higher-order complexes beyond the 3:2 stoichiometry, but not yet documented, are involved in the formation of SynGAP/PSD-95 condensates, imploring future efforts to ascertain the nature of these auxiliary interactions in PSD-like LLPS.

q-bio.BM↗

arXiv2021

The Calderón problem for the fractional wave equation: Uniqueness and optimal stability

We study an inverse problem for the fractional wave equation with a potential by the measurement taking on arbitrary subsets of the exterior in the space-time domain. We are interested in the issues of uniqueness and stability estimate in the determination of the potential by the exterior Dirichlet-to-Neumann map. The main tools are the qualitative and quantitative unique continuation properties for the fractional Laplacian. For the stability, we also prove that the log type stability estimate is optimal. The log type estimate shows the striking difference between the inverse problems for the fractional and classical wave equations in the stability issue. The results hold for any spatial dimension $n\in \N$.

math.AP↗

arXiv2021

A Simple Explicit-Solvent Model of Polyampholyte Phase Behaviors and its Ramifications for Dielectric Effects in Biomolecular Condensates

Biomolecular condensates such as membraneless organelles, underpinned by liquid-liquid phase separation (LLPS), are important for physiological function, with electrostatics -- among other interaction types -- being a prominent force in their assembly. Charge interactions of intrinsically disordered proteins (IDPs) and other biomolecules are sensitive to the aqueous dielectric environment. Because the relative permittivity of protein is significantly lower than that of water, the interior of an IDP condensate is a relatively low-dielectric regime, which, aside from its possible functional effects on client molecules, should facilitate stronger electrostatic interactions among the scaffold IDPs. To gain insight into this LLPS-induced dielectric heterogeneity, addressing in particular whether a low-dielectric condensed phase entails more favorable LLPS than that posited by assuming IDP electrostatic interactions are uniformly modulated by the higher dielectric constant of the pure solvent, we consider a simplified multiple-chain model of polyampholytes immersed in explicit solvents that are either polarizable or possess a permanent dipole. Notably, simulated phase behaviors of these systems exhibit only minor to moderate differences from those obtained using implicit-solvent models with a uniform relative permittivity equals to that of pure solvent. Buttressed by theoretical treatments developed here using random phase approximation and polymer field-theoretic simulations, these observations indicate a partial compensation of effects between favorable solvent-mediated interactions among the polyampholytes in the condensed phase and favorable polyampholyte-solvent interactions in the dilute phase, often netting only a minor enhancement of overall LLPS propensity from the very dielectric heterogeneity that arises from the LLPS itself. Further ramifications of this principle are discussed.

q-bio.BM↗

arXiv2020

Inverse problems for elliptic equations with fractional power type nonlinearities

We study inverse problems for semilinear elliptic equations with fractional power type nonlinearities. Our arguments are based on the higher order linearization method, which helps us to solve inverse problems for certain nonlinear equations in cases where the solution for a corresponding linear equation is not known. By using a fractional order adaptation of this method, we show that the results of [LLLS20a, LLLS20b] remain valid for general power type nonlinearities.

math.AP↗

arXiv2020

Monotonicity-based inversion of fractional semilinear elliptic equations with power type nonlinearities

We investigate the monotonicity method for fractional semilinear elliptic equations with power type nonlinearities. We prove that if-and-only-if monotonicity relations between coefficients and the derivative of the Dirichlet-to-Neumann map hold. Based on the strong monotonicity relations, we study a constructive global uniqueness for coefficients and inclusion detection for the fractional Calderón type inverse problem. Meanwhile, we can also derive the Lipschitz stability with finitely many measurements. The results hold for any $n\geq 1$.

math.AP↗

arXiv2020

Comparative Roles of Charge, $π$ and Hydrophobic Interactions in Sequence-Dependent Phase Separation of Intrinsically Disordered Proteins

Endeavoring toward a transferable, predictive coarse-grained explicit-chain model for biomolecular condensates underlain by liquid-liquid phase separation (LLPS), we conducted multiple-chain simulations of the N-terminal intrinsically disordered region (IDR) of DEAD-box helicase Ddx4, as a test case, to assess the roles of electrostatic, hydrophobic, cation-$π$, and aromatic interactions in amino acid sequence-dependent LLPS. We evaluated 3 residue-residue interaction schemes with a shared electrostatic potential. Neither a common hydrophobicity scheme nor one augmented with arginine/lysine-aromatic cation-$π$ interactions consistently accounted for the experimental LLPS data on the wildtype, a charge-scrambled, an FtoA, and an RtoK mutant of Ddx4 IDR. In contrast, interactions based on contact statistics among folded globular protein structures reproduce the overall experimental trend, including that the RtoK mutant has a much diminished LLPS propensity. Consistency between simulation and LLPS experiment was also found for RtoK mutants of P-granule protein LAF-1, underscoring that, to a degree, the important LLPS-driving $π$-related interactions are embodied in classical statistical potentials. Further elucidation will be necessary, however, especially of phenylalanine's role in condensate assembly because experiments on FtoA and YtoF mutants suggest that LLPS-driving phenylalanine interactions are significantly weaker than those posited by common statistical potentials. Protein-protein electrostatic interactions are modulated by relative permittivity, which depends on protein concentration. Analytical theory suggests that this dependence entails enhanced inter-protein interactions in the condensed phase but more favorable protein-solvent interactions in the dilute phase. The opposing trends lead to a modest overall impact on LLPS.

q-bio.BM↗

arXiv2020

Random Non-Expected Utility: Non-Uniqueness

In random expected utility (Gul and Pesendorfer, 2006), the distribution of preferences is uniquely recoverable from random choice. This paper shows through two examples that such uniqueness fails in general if risk preferences are random but do not conform to expected utility theory. In the first, non-uniqueness obtains even if all preferences are confined to the betweenness class (Dekel, 1986) and are suitably monotone. The second example illustrates random choice behavior consistent with random expected utility that is also consistent with random non-expected utility. On the other hand, we find that if risk preferences conform to weighted utility theory (Chew, 1983) and are monotone in first-order stochastic dominance, random choice again uniquely identifies the distribution of preferences. Finally, we argue that, depending on the domain of risk preferences, uniqueness may be restored if joint distributions of choice across a limited number of feasible sets are available.

econ.TH↗

arXiv2020

A direct reconstruction algorithm for the anisotropic inverse conductivity problem based on Calderón's method in the plane

A direct reconstruction algorithm based on Calderón's linearization method for the reconstruction of isotropic conductivities is proposed for anisotropic conductivities in two-dimensions. To overcome the non-uniqueness of the anisotropic inverse conductivity problem, the entries of the unperturbed anisotropic tensors are assumed known \emph{a priori}, and it remains to reconstruct the multiplicative scalar field. The quasi-conformal map in the plane facilitates the Calderón-based approach for anisotropic conductivities. The method is demonstrated on discontinuous radially symmetric conductivities of high and low contrast.

math.NA↗

arXiv2020

Analytical Theory for Sequence-Specific Binary Fuzzy Complexes of Charged Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) are important for biological functions. In contrast to folded proteins, molecular recognition among certain IDPs is "fuzzy" in that their binding and/or phase separation are stochastically governed by the interacting IDPs' amino acid sequences while their assembled conformations remain largely disordered. To help elucidate a basic aspect of this fascinating yet poorly understood phenomenon, the binding of a homo- or hetero-dimeric pair of polyampholytic IDPs is modeled statistical mechanically using cluster expansion. We find that the binding affinities of binary fuzzy complexes in the model correlate strongly with a newly derived simple "jSCD" parameter readily calculable from the pair of IDPs' sequence charge patterns. Predictions by our analytical theory are in essential agreement with coarse-grained explicit-chain simulations. This computationally efficient theoretical framework is expected to be broadly applicable to rationalizing and predicting sequence-specific IDP-IDP polyelectrostatic interactions.

q-bio.BM↗

arXiv2020

Duality between range and no-response tests and its application for inverse problems

In this paper we will show the duality between the range test (RT) and no-response test (NRT) for the inverse boundary value problem for the Laplace equation in $Ω\setminus\overline D$ with an obstacle $D\SubsetΩ$ whose boundary $\partial D$ is visible from the boundary $\partialΩ$ of $Ω$ and a measurement is given as a set of Cauchy data on $\partialΩ$. Here the Cauchy data is given by a unique solution $u$ of the boundary value problem for the Laplace equation in $Ω\setminus\overline D$ with homogeneous and inhomogeneous Dirichlet boundary condition on $\partial D$ and $\partialΩ$, respectively. These testing methods are domain sampling method to estimate the location of the obstacle using test domains and the associated indicator functions. Also both of these testing methods can test the analytic extension of $u$ to the exterior of a test domain. Since these methods are defined via some operators which are dual to each other, we could expect that there is a duality between the two methods. We will give this duality in terms of the equivalence of the pre-indicator functions associated to their indicator functions. As an application of the duality, the reconstruction of $D$ using the RT gives the reconstruction of $D$ using the NRT and vice versa. We will also give each of these reconstructions without using the duality if the Dirichlet data of the Cauchy data on $\partialΩ$ is not identically zero and the solution to the associated forward problem does not have any analytic extension across $\partial D$. Moreover, we will show that these methods can still give the reconstruction of $D$ if $D$ is a convex polygon and it satisfies one of the following two properties: all of its corner angles are irrational and its diameter is less than its distance to $\partialΩ$.

math.AP↗

arXiv2020

Inverse problems for fractional semilinear elliptic equations

This paper is concerned with the forward and inverse problems for the fractional semilinear elliptic equation $(-Δ)^s u +a(x,u)=0$ for $0<s<1$. For the forward problem, we proved the problem is well-posed and has a unique solution for small exterior data. The inverse problems we consider here consists of two cases. First we demonstrate that an unknown coefficient $a(x,u)$ can be uniquely determined from the knowledge of exterior measurements, known as the Dirichlet-to-Neumann map. Second, despite the presence of an unknown obstacle in the media, we show that the obstacle and the coefficient can be recovered concurrently from these measurements. Finally, we investigate that these two fractional inverse problems can also be solved by using a single measurement, and all results hold for any dimension $n\geq 1$.

math.AP↗

arXiv2020

Monotonicity-based inversion of the fractional Schrödinger equation II. General potentials and stability

In this work, we use monotonicity-based methods for the fractional Schrödinger equation with general potentials $q\in L^\infty(Ω)$ in a Lipschitz bounded open set $Ω\subset \mathbb R^n$ in any dimension $n\in \mathbb N$. We demonstrate that if-and-only-if monotonicity relations between potentials and the Dirichlet-to-Neumann map hold up to a finite dimensional subspace. Based on these if-and-only-if monotonicity relations, we derive a constructive global uniqueness results for the fractional Calderón problem and its linearized version. We also derive a reconstruction method for unknown obstacles in a given domain that only requires the background solution of the fractional Schrödinger equation, and we prove uniqueness and Lipschitz stability from finitely many measurements for potentials lying in an a-priori known bounded set in a finite dimensional subset of $L^\infty(Ω)$.

math.AP↗