@inbook{18167, abstract = {Holdase chaperones are essential in the mitochondrial membrane-protein biogenesis as they stabilize preproteins and keep them in an import-competent state as they travel through the aqueous cytosol and intermembrane space. The small TIM chaperones of the mitochondrial intermembrane space function within a fine balance of client promiscuity and high affinity binding, while being also able to release their client proteins without significant energy barrier to the downstream insertases/translocases. The tendency of the preproteins to aggregate and the dynamic nature of the preprotein—chaperone complexes makes the preparation of these complexes challenging. Here we present two optimized methods for complex formation of highly hydrophobic precursor proteins and chaperones: a pull-down approach and an in-vitro translation strategy. In the former, attaching the client protein to an affinity resin keeps the individual client protein copies apart from each other and decreases the client self-aggregation probability, thereby favouring complex formation. In the latter approach, a purified chaperone, added to the cell-free protein synthesis, captures the nascent precursor protein. The choice of method will depend on the desired client-chaperone complex amount, or the need for specific labeling scheme.}, author = {Guillerm, Undina and Sučec, Iva and Schanda, Paul}, booktitle = {Methods in Enzymology}, issn = {0076-6879}, pages = {391--422}, publisher = {Elsevier}, title = {{Generation of TIM chaperone substrate complexes}}, doi = {10.1016/bs.mie.2024.07.051}, volume = {707}, year = {2024}, } @article{18187, abstract = {Quasicrystals are ordered but not periodic, which makes them fascinating objects at the interface between order and disorder. Experiments with ultracold atoms zoom in on this interface by driving a quasicrystal and exploring its fractal properties.}, author = {Leonard, Julian}, issn = {1745-2481}, journal = {Nature Physics}, number = {3}, pages = {351--352}, publisher = {Springer Nature}, title = {{A kicked quasicrystal}}, doi = {10.1038/s41567-023-02357-0}, volume = {20}, year = {2024}, } @article{18188, abstract = {New generations of ultracold-atom experiments are continually raising the demand for efficient solutions to optimal control problems. Here, we apply Bayesian optimization to improve a state-preparation protocol recently implemented in an ultracold-atom system to realize a two-particle fractional quantum Hall state. Compared to manual ramp design, we demonstrate the superior performance of our optimization approach in a numerical simulation – resulting in a protocol that is 10x faster at the same fidelity, even when taking into account experimentally realistic levels of disorder in the system. We extensively analyze and discuss questions of robustness and the relationship between numerical simulation and experimental realization, and how to make the best use of the surrogate model trained during optimization. We find that numerical simulation can be expected to substantially reduce the number of experiments that need to be performed with even the most basic transfer learning techniques. The proposed protocol and workflow will pave the way toward the realization of more complex many-body quantum states in experiments.}, author = {Blatz, Tizian and Kwan, Joyce and Leonard, Julian and Bohrdt, Annabelle}, issn = {2521-327X}, journal = {Quantum}, publisher = {Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften}, title = {{Bayesian optimization for robust state preparation in quantum many-body systems}}, doi = {10.22331/q-2024-06-27-1388}, volume = {8}, year = {2024}, } @unpublished{18202, abstract = {We report on adiabatic state preparation in the one-dimensional quantum Ising model using ultracold bosons in a tilted optical lattice. We prepare many-body ground states of controllable system sizes and observe enhanced fluctuations around the transition between paramagnetic and antiferromagnetic states, marking the precursor of quantum critical behavior. Furthermore, we find evidence for superpositions of domain walls and study their effect on the many-body ground state by measuring the populations of each spin configuration across the transition. These results shed new light on the effect of boundary conditions in finite-size quantum systems.}, author = {Kim, Sooshin and Lukin, Alexander and Rispoli, Matthew and Tai, M. Eric and Kaufman, Adam M. and Segura, Perrin and Li, Yanfei and Kwan, Joyce and Leonard, Julian and Brice Bakkali-Hassani, Brice Bakkali-Hassani and Greiner, Markus}, booktitle = {arXiv}, title = {{Adiabatic state preparation in a quantum Ising spin chain}}, doi = {10.48550/arXiv.2404.07481}, year = {2024}, } @article{18203, abstract = {Protein Data Bank (PDB) files list the relative spatial location of atoms in a protein structure as the final output of the process of fitting and refining to experimentally determined electron density measurements. Where experimental evidence exists for multiple conformations, atoms are modelled in alternate locations. Programs reading PDB files commonly ignore these alternate conformations by default leaving users oblivious to the presence of alternate conformations in the structures they analyze. This has led to underappreciation of their prevalence, under characterisation of their features and limited the accessibility to this high-resolution data representing structural ensembles. We have trawled PDB files to extract structural features of residues with alternately located atoms. The output includes the distance between alternate conformations and identifies the location of these segments within the protein chain and in proximity of all other atoms within a defined radius. This dataset should be of use in efforts to predict multiple structures from a single sequence and support studies investigating protein flexibility and the association with protein function.}, author = {Rosenberg, Aviv A. and Marx, Ailie and Bronstein, Alexander}, issn = {2052-4463}, journal = {Scientific Data}, publisher = {Springer Nature}, title = {{A dataset of alternately located segments in protein crystal structures}}, doi = {10.1038/s41597-024-03595-4}, volume = {11}, year = {2024}, } @article{18204, abstract = {Non-linear dynamical systems describe numerous real-world phenomena, ranging from the weather, to financial markets and disease progression. Individual systems may share substantial common information, for example patients’ anatomy. Lately, deep-learning has emerged as a leading method for data-driven modeling of non-linear dynamical systems. Yet, despite recent breakthroughs, prior works largely ignored the existence of shared information between different systems. However, such cases are quite common, for example, in medicine: we may wish to have a patient-specific model for some disease, but the data collected from a single patient is usually too small to train a deep-learning model. Hence, we must properly utilize data gathered from other patients. Here, we explicitly consider such cases by jointly modeling multiple systems. We show that the current single-system models consistently fail when trying to learn simultaneously from multiple systems. We suggest a framework for jointly approximating the Koopman operators of multiple systems, while intrinsically exploiting common information. We demonstrate how we can adapt to a new system using order-of-magnitude less new data and show the superiority of our model over competing methods, in terms of both forecasting ability and statistical fidelity, across chaotic, cardiac, and climate systems.}, author = {Elul, Yonatan and Rozenberg, Eyal and Boyarski, Amit and Yaniv, Yael and Schuster, Assaf and Bronstein, Alexander}, issn = {2399-3650}, journal = {Communications Physics}, publisher = {Springer Nature}, title = {{Data-driven modeling of interrelated dynamical systems}}, doi = {10.1038/s42005-024-01626-5}, volume = {7}, year = {2024}, } @article{18205, abstract = {We explore numerically an unsupervised, physics-informed, deep learning-based reconstruction technique for time-resolved imaging by multiplexed ptychography. In our method, the untrained deep learning model replaces the iterative algorithm’s update step, yielding superior reconstructions of multiple dynamic object frames compared to conventional methodologies. More precisely, we demonstrate improvements in image quality and resolution, while reducing sensitivity to the number of recorded frames, the mutual orthogonality of different probe modes, overlap between neighboring probe beams and the cutoff frequency of the ptychographic microscope – properties that are generally of paramount importance for ptychographic reconstruction algorithms.}, author = {Wengrowicz, Omri and Bronstein, Alexander and Cohen, Oren}, issn = {1094-4087}, journal = {Optics Express}, number = {6}, pages = {8791--8803}, publisher = {Optica Publishing Group}, title = {{Unsupervised physics-informed deep learning-based reconstruction for time-resolved imaging by multiplexed ptychography}}, doi = {10.1364/oe.515445}, volume = {32}, year = {2024}, } @inproceedings{18206, abstract = {In the context of in vitro fertilization (IVF), selecting embryos for transfer is critical in determining pregnancy outcomes, with implantation as the essential first milestone for a successful pregnancy. This study introduces the Bonna algorithm, an advanced deep-learning framework engineered to predict embryo implantation probabilities. The algorithm employs a sophisticated integration of machine-learning techniques, utilizing MobileNetV2 for pixel and context embedding, a custom Pix2Pix model for precise segmentation, and a Vision Transformer for additional depth in embedding. MobileNetV2 was chosen for its robust feature extraction capabilities, focusing on textures and edges. The custom Pix2Pix model is adapted for precise segmentation of significant biological features such as the zona pellucida and blastocyst cavity. The Vision Transformer adds a global perspective, capturing complex patterns not apparent in local image segments. Tested on a dataset of images of human blastocysts collected from Ukraine, Israel, and Spain, the Bonna algorithm was rigorously validated through 10-fold cross-validation to ensure its robustness and reliability. It demonstrates superior performance with a mean area under the receiver operating characteristic curve (AUC) of 0.754, significantly outperforming existing models. The study not only advances predictive accuracy in embryo selection but also highlights the algorithm’s clinical applicability due to reliable confidence reporting.}, author = {Rave, Gilad and Fordham, Daniel E. and Bronstein, Alexander and Silver, David H.}, booktitle = {First International Conference on Artificial Intelligence in Healthcare}, isbn = {9783031672842}, issn = {1611-3349}, location = {Swansea, United Kingdom}, pages = {160--171}, publisher = {Springer Nature}, title = {{Enhancing predictive accuracy in embryo implantation: The Bonna algorithm and its clinical implications}}, doi = {10.1007/978-3-031-67285-9_12}, volume = {14976}, year = {2024}, } @article{22065, abstract = {The Benjamin–Ono equation is shown to be well-posed, both on the line and on the circle, in the Sobolev spaces H^s for s > -1/2. The proof rests on a new gauge transformation and benefits from our introduction of a modified Lax pair representation of the full hierarchy. As we will show, these developments yield important additional dividends beyond well-posedness, including (i) the unification of the diverse approaches to polynomial conservation laws; (ii) a generalization of Gérard’s explicit formula to the full hierarchy; and (iii) new virial-type identities covering all equations in the hierarchy.}, author = {Killip, Rowan and Laurens, Thierry and Visan, Monica}, issn = {1432-1297}, journal = {Inventiones mathematicae}, number = {3}, pages = {999--1054}, publisher = {Springer Nature}, title = {{Sharp well-posedness for the Benjamin–Ono equation}}, doi = {10.1007/s00222-024-01250-8}, volume = {236}, year = {2024}, } @article{22062, abstract = {We prove that the derivative nonlinear Schrödinger equation in one space dimension is globally well-posed on the line in L^2 (R), which is the scaling-critical space for this equation.}, author = {Harrop-Griffiths, Benjamin and Killip, Rowan and Ntekoume, Maria and Visan, Monica}, issn = {1435-9863}, journal = {Journal of the European Mathematical Society}, number = {2}, pages = {843--924}, publisher = {EMS Press}, title = {{Global well-posedness for the derivative nonlinear Schrödinger equation in L^2(R)}}, doi = {10.4171/jems/1490}, volume = {28}, year = {2024}, } @article{22074, abstract = {We discuss how countable subadditivity of operators can be derived from subadditivity under mild forms of continuity, and provide examples manifesting such circumstances.}, author = {Grafakos, Loukas and Visan, Monica}, issn = {1473-7124}, journal = {Proceedings of the Royal Society of Edinburgh: Section A Mathematics}, number = {5}, pages = {1504--1517}, publisher = {Cambridge University Press}, title = {{Remarks on countable subadditivity}}, doi = {10.1017/prm.2023.77}, volume = {154}, year = {2024}, } @article{22079, abstract = {We prove that the cubic nonlinear Schrödinger equation (both focusing and defocusing) is globally well-posed in H^s(R) for any regularity s > −1/2. Well-posedness has long been known for s ≥ 0, see [55], but not previously for any s < 0. The scaling-critical value s = −1/2 is necessarily excluded here, since instantaneous norm inflation is known to occur [11, 40, 48]. We also prove (in a parallel fashion) well-posedness of the real- and complex-valued modified Korteweg–de Vries equations in H^s(R) for any s > −1/2. The best regularity achieved previously was s ≥ 1/4 (see [15, 24, 33, 39]). To overcome the failure of uniform continuity of the data-to-solution map, we employ the method of commuting flows introduced in [37]. In stark contrast with our arguments in [37], an essential ingredient in this paper is the demonstration of a local smoothing effect for both equations. Despite the nonperturbative nature of the well-posedness, the gain of derivatives matches that of the underlying linear equation. To compensate for the local nature of the smoothing estimates, we also demonstrate tightness of orbits. The proofs of both local smoothing and tightness rely on our discovery of a new one-parameter family of coercive microscopic conservation laws that remain meaningful at this low regularity. }, author = {Harrop-Griffiths, Benjamin and Killip, Rowan and Visan, Monica}, issn = {2050-5086}, journal = {Forum of Mathematics, Pi}, publisher = {Cambridge University Press}, title = {{Sharp well-posedness for the cubic NLS and mKdV in H^s(R)}}, doi = {10.1017/fmp.2024.4}, volume = {12}, year = {2024}, } @article{22123, abstract = {Frontal ablation is responsible for a large fraction of the mass loss from tidewater glaciers. The main contributors to frontal ablation are iceberg calving and submarine melting, with calving often being the largest. However, submarine melting, in addition to its direct contribution to mass loss, also promotes calving through the changes induced in the stress field at the glacier terminus, so both processes should be jointly analysed. Among the factors influencing submarine melting, the formation of a buoyant plume due to the emergence of fresh subglacial water at the glacier grounding line plays a key role. In this study we used Elmer/Ice to develop a 3D glacier dynamics model including calving and subglacial hydrology coupled with a line plume model to calculate the calving front position at every time step. We applied this model to the Hansbreen–Hansbukta glacier–fjord system in southern Spitsbergen, Svalbard, where a large set of data are available for both the glacier and the fjord from September 2008 to March 2011. We found that our 3D model reproduced the expected seasonal cycle of advance–retreat. Besides, the modelled front positions were in good agreement with the observed front positions at the central part of the calving front, with longitudinal differences, on average, below 15 m for the period from December 2009 to March 2011. But there were regions of the front, especially the eastern margin, that presented major differences.}, author = {Muñoz Hermosilla, José M and Otero, Jaime and De Andrés, Eva and Shahateet, Kaian and Navarro, Francisco and Pérez-Doña, Iván}, issn = {1994-0424}, journal = {The Cryosphere}, number = {4}, pages = {1911--1924}, publisher = {Copernicus Publications}, title = {{A 3D glacier dynamics–line plume model to estimate the frontal ablation of Hansbreen, Svalbard}}, doi = {10.5194/tc-18-1911-2024}, volume = {18}, year = {2024}, } @unpublished{20701, abstract = {A Proof of Exponentiation (PoE) allows a prover to efficiently convince a verifier that 𝑦 = 𝑥 𝑒 in some group of unknown order. PoEs are the basis for practical constructions of Verifiable Delay Functions (VDFs), which, in turn, are important for various higher-level protocols in distributed computing. In applications such as distributed consensus, many PoEs are generated regularly, motivating protocols for secure aggregation of batches of statements into a few statements to improve the efficiency for both parties. Rotem (TCC 2021) recently presented two such generic batch PoEs. In this work, we introduce two batch PoEs that outperform both proposals of Rotem and we evaluate their practicality. First, we show that the two batch PoEs of Rotem can be combined to improve the overall efficiency by at least a factor of two. Second, we revisit the work of Bellare, Garay, and Rabin (EUROCRYPT 1998) on batch verification of digital signatures and show that, under the low order assumption, their bucket test can be securely adapted to the setting of groups of unknown order. The resulting batch PoE quickly outperforms the state of the art in the expected number of group multiplications with the growing number of instances, and it decreases the cost of batching by an order of magnitude already for hundreds of thousands of instances. Importantly, it is the first batch PoE that significantly decreases both the proof size and complexity of verification. Our experimental evaluations show that even a nonoptimized implementation achieves such improvements, which would match the demands of real-life systems requiring large-scale PoE processing. Finally, even though our proof techniques are conceptually similar to Rotem, we give an improved analysis of the application of the low order assumption towards secure batching of PoE instances, resulting in a tight reduction, which is important when setting the security parameter in practice.}, author = {Hoffmann, Charlotte and Hubáček, Pavel and Ivanova, Svetlana}, booktitle = {Cryptology ePrint Archive}, publisher = {International Association for Cryptologic Research}, title = {{Practical batch proofs of exponentiation}}, year = {2024}, } @article{22154, abstract = {The inertia bound and ratio bound (also known as the Cvetković bound and Hoffman bound) are two fundamental inequalities in spectral graph theory, giving upper bounds on the independence number a(G) of a graph G in terms of spectral information about a weighted adjacency matrix of G. For both inequalities, given a graph G, one needs to make a judicious choice of weighted adjacency matrix to obtain as strong a bound as possible. While there is a well‐established theory surrounding the ratio bound, the inertia bound is much more mysterious, and its limits are rather unclear. In fact, only recently did Sinkovic find the first example of a graph for which the inertia bound is not tight (for any weighted adjacency matrix), answering a longstanding question of Godsil. We show that the inertia bound can be extremely far from tight, and in fact can significantly underperform the ratio bound: for example, one of our results is that for infinitely many n, there is an n‐vertex graph for which even the unweighted ratio bound can prove a(G)<4n^3/4, but the inertia bound is always at least n/4. In particular, these results address questions of Rooney, Sinkovic, and Wocjan–Elphick–Abiad.}, author = {Kwan, Matthew and Wigderson, Yuval}, issn = {1469-2120}, journal = {Bulletin of the London Mathematical Society}, number = {10}, pages = {3196--3208}, publisher = {Wiley}, title = {{The inertia bound is far from tight}}, doi = {10.1112/blms.13127}, volume = {56}, year = {2024}, } @article{22179, abstract = {Burr and Erd˝os in 1975 conjectured, and Chv´atal, R¨odl, Szemer´edi and Trotter later proved, that the Ramsey number of any bounded degree graph is linear in the number of vertices. In this paper, we disprove the natural directed analogue of the Burr–Erd˝os conjecture, answering a question of Buci´c, Letzter, and Sudakov. If H is an acyclic digraph, the oriented Ramsey number of H, denoted −→r1(H), is the least N such that every tournament on N vertices contains a copy of H. We show that for any Δ ≥ 2 and any sufficiently large n, there exists an acyclic digraph H with n vertices and maximum degree Δ such that −→r1(H) ≥ nΩ(Δ2/3/ log5/3 Δ). This proves that −→r1(H) is not always linear in the number of vertices for bounded-degree H. On the other hand, we show that −→r1(H) is nearly linear in the number of vertices for typical bounded-degree acyclic digraphs H, and obtain linear or nearly linear bounds for several natural families of bounded-degree acyclic digraphs. For multiple colors, we prove a quasi-polynomial upper bound −→rk(H)= 2(log n)Ok(1) for all bounded-degree acyclic digraphs H on n vertices, where −→rk(H) is the least N such that every k-edge-colored tournament on N vertices contains a monochromatic copy of H. For k ≥ 2 and n ≥ 4, we exhibit an acyclic digraph H with n vertices and maximum degree 3 such that −→rk(H) ≥ nΩ(log n/ log log n), showing that these Ramsey numbers can grow faster than any polynomial in the number of vertices.}, author = {Fox, Jacob and He, Xiaoyu and Wigderson, Yuval}, issn = {1565-8511}, journal = {Israel Journal of Mathematics}, number = {1}, pages = {1--48}, publisher = {Springer Nature}, title = {{Ramsey numbers of sparse digraphs}}, doi = {10.1007/s11856-024-2624-y}, volume = {263}, year = {2024}, } @article{22180, abstract = {Given a graph , its Ramsey number is the minimum so that every two‐coloring of contains a monochromatic copy of . It was conjectured by Conlon, Fox, and Sudakov that if one deletes a single vertex from , the Ramsey number can change by at most a constant factor. We disprove this conjecture, exhibiting an infinite family of graphs such that deleting a single vertex from each decreases the Ramsey number by a super‐constant factor. One consequence of this result is the following. There exists a family of graphs so that in any Ramsey coloring for (i.e., a coloring of a clique on vertices with no monochromatic copy of ), one of the color classes has density .}, author = {Wigderson, Yuval}, issn = {1097-0118}, journal = {Journal of Graph Theory}, number = {3}, pages = {663--675}, publisher = {Wiley}, title = {{Ramsey numbers upon vertex deletion}}, doi = {10.1002/jgt.23093}, volume = {106}, year = {2024}, } @article{22190, abstract = {We consider the set of 𝑚×𝑛 matrices with rational entries having numerator and denominator of size at most H and obtain various upper bounds on the number of such matrices of a given rank, or with a given determinant, or a given characteristic polynomial. We also consider similar questions for matrices whose entries are Egyptian fractions.}, author = {Afifurrahman, Muhammad and Kuperberg, Vivian Zieve and Ostafe, Alina and Shparlinski, Igor E.}, issn = {1435-5337}, journal = {Forum Mathematicum}, number = {4}, publisher = {De Gruyter}, title = {{Statistics of ranks, determinants and characteristic polynomials of rational matrices}}, doi = {10.1515/forum-2024-0114}, volume = {37}, year = {2024}, } @article{22197, abstract = {We study the distribution of consecutive sums of two squares in arithmetic progressions. If {En}n∈N is the sequence of sums of two squares in increasing order, we show that for any modulus q and any congruence classes a1, a2, a3 mod q which are admissible in the sense that there are solutions to x2 + y2 ≡ ai mod q, there exist infinitely many n with En+i−1 ≡ ai mod q, for i =1, 2, 3. We also show that for any r1, r2 ≥ 1, there exist infinitely many n with En+i−1 ≡ a1 mod q for 1 ≤ i ≤ r1 and En+i−1 ≡ a2 mod q for r1 +1 ≤ i ≤ r1 + r2}, author = {Kimmel, Noam and Kuperberg, Vivian Zieve}, issn = {0022-314X}, journal = {Journal of Number Theory}, pages = {135--147}, publisher = {Elsevier}, title = {{Consecutive runs of sums of two squares}}, doi = {10.1016/j.jnt.2024.05.003}, volume = {264}, year = {2024}, } @article{22209, abstract = {The curvature of elongated microscopic building blocks plays a crucial role on their self-assembly into orientationally ordered phases. While rod-like molecules form a handful of liquid crystal (LC) phases, curved or banana-shaped molecules show more than fifty phases, with fascinating physical properties, such as chirality or polarity. Despite the fundamental and technological importance of these so-called ‘banana-shaped liquid crystals’, little is known about their microscopic details at the single-molecule level. Curved colloidal liquid crystals—liquid crystals formed by curved colloidal rods—are excellent model systems to optically resolve the structure and dynamics of curved building blocks within these condensed phases. Recent advances in the synthesis of curved rod-like particles have unlocked the potential for studying—at the single-particle level—the intimate relationship between shape and phase symmetry, and even confirmed the stability of elusive LC phases. Further developments in this nascent field promise exciting findings, such as the first observation of the colloidal twist-bend nematic phase or the fabrication of functional materials with curvature-dependent properties. In this Report on Progress, we will highlight recent advances in the synthesis and assembly of curved colloidal liquid crystals and discuss the upcoming challenges and opportunities of this field.}, author = {Fernández-Rico, Carla and Dullens, Roel P A}, issn = {1361-6633}, journal = {Reports on Progress in Physics}, number = {9}, publisher = {IOP Publishing}, title = {{Liquid crystals from curved colloidal rods: Waves, twists and more}}, doi = {10.1088/1361-6633/ad627b}, volume = {87}, year = {2024}, }