arXiv subjects

Michael Slutsky

Publications and source records attributed to Michael Slutsky.

5 recordsLinked to original sources

arXiv2026

Blueprint for a fault-tolerant compound photon-atom quantum architecture

Fault-tolerant quantum computing requires architectures that simultaneously address scalability, connectivity, and error correction under realistic noise constraints. We present a compound photonic-atomic quantum computing platform that uses cavity QED to realize near-deterministic entangling operations between flying photonic qubits and stationary atomic qubits. Photons provide long-range connectivity and scalability via measurement-based quantum computing (MBQC), while atoms supply reusable, near-deterministic resources for photon generation and entanglement, overcoming the inefficiency of purely photonic platforms. The core primitive is a symmetrized Duan-Kimble photon-atom controlled-phase (CZ) gate, robust to experimental imperfections and high-fidelity. Using single $^{87}$Rb atoms coupled to optical cavities, we give protocols for state preparation, measurement, photon generation, and entangling gates on tens-of-nanosecond timescales, and show how large-scale cluster states with effectively unrestricted connectivity and reduced overhead can be generated through atomic reuse. We analyze fault tolerance on the Raussendorf-Harrington-Goyal (RHG) lattice with a hardware-aware noise model capturing asymmetric loss and correlated photonic-atomic errors. Logical memory simulations yield a photon-loss threshold near $2.6\%$ per physical gate ($\sim$15\% total per trajectory). The full Clifford set -- Hadamard, phase, CNOT -- is implementable transversally or fold-transversally at thresholds matching the identity channel, and we propose two non-Clifford resource-state routes (code teleportation and magic state cultivation) within the foliated cluster-state architecture.

quant-ph↗

arXiv2004

Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential

Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a long DNA molecule and then strongly binds this site. Here we aim to find a mechanism that can provide both a fast search (1-10 sec) and high stability of the specific protein-DNA complex ($K_d=10^{-15}-10^{-8}$ M). Earlier studies have suggested that rapid search involves the sliding of a protein along the DNA. Here we consider sliding as a one-dimensional (1D) diffusion in a sequence-dependent rough energy landscape. We demonstrate that, in spite of the landscape's roughness, rapid search can be achieved if 1D sliding is accompanied by 3D diffusion. We estimate the range of the specific and non-specific DNA-binding energy required for rapid search and suggest experiments that can test our mechanism. We show that optimal search requires a protein to spend half of time sliding along the DNA and half diffusing in 3D. We also establish that, paradoxically, realistic energy functions cannot provide both rapid search and strong binding of a rigid protein. To reconcile these two fundamental requirements we propose a search-and-fold mechanism that involves the coupling of protein binding and partial protein folding. Proposed mechanism has several important biological implications for search in the presence of other proteins and nucleosomes, simultaneous search by several proteins etc. Proposed mechanism also provides a new framework for interpretation of experimental and structural data on protein-DNA interactions.

q-bio.BM↗

arXiv2004

Apex Exponents for Polymer--Probe Interactions

We consider self-avoiding polymers attached to the tip of an impenetrable probe. The scaling exponents $γ_1$ and $γ_2$, characterizing the number of configurations for the attachment of the polymer by one end, or at its midpoint, vary continuously with the tip's angle. These apex exponents are calculated analytically by $ε$-expansion, and numerically by simulations in three dimensions. We find that when the polymer can move through the attachment point, it typically slides to one end; the apex exponents quantify the entropic barrier to threading the eye of the probe.

cond-mat.stat-mech↗

arXiv2004

Diffusion in a Half-Space: From Lord Kelvin to Path Integrals

Many important transport phenomena are described by simple mathematical models rooted in the diffusion equation. Geometrical constraints present in such phenomena often have influence of a universal sort and manifest themselves in scaling relations and stable distribution functions. In this paper, I present a treatment of a random walk confined to a half--space using a number of different approaches: diffusion equations, lattice walks and path integrals. Potential generalizations are discussed critically.

cond-mat.stat-mech↗

arXiv2003

The long reach of DNA sequence heterogeneity in diffusive processes

Many biological processes involve one dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length $ξ_c$. Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA translocation through a nanopore, in all cases with $ξ_c\approx$ 10 nm. We investigate such transport processes by the mean first passage time (MFPT) formalism, and find diffusion times which exhibit strong sample to sample fluctuations. For a a displacement $N$, the average MFPT is diffusive, while its standard deviation over the ensemble of energy profiles scales as $N^{3/2}$ with a large prefactor. Fluctuations are thus dominant for displacements smaller than a characteristic $N_c \gg ξ_c$: typical values are much less than the mean, and governed by an anomalous diffusion rule. Potential biological consequences of such random walks, composed of rapid scans in the vicinity of favorable energy valleys and occasional jumps to further valleys, is discussed.

q-bio.BM↗