Monte Carlo algorithms based on the number of potential moves

We discuss Monte Carlo dynamics based on _E, the (microcanonical) average number of potential moves which increase the energy by Delta E in a single spin flip. The microcanonical average can be sampled using Monte Carlo dynamics of a single spin flip with a transition rate min(1, _E' / _E) from energy E to E'. A cumulative average (over Monte Carlo steps) can be used as a first approximation to the exact microcanonical average in the flip rate. The associated histogram is a constant independent of the energy. The canonical distribution of energy can be obtained from the transition matrix Monte Carlo dynamics. This second dynamics has fast relaxation time - at the critical temperature the relaxation time is proportional to specific heat. The dynamics are useful in connection with reweighting methods for computing thermodynamic quantities.Comment: 8 pages, 4 figures, invited talk on CCP99 conference, 20-27 May 99, Atlanta, G

Heat Conduction in two-dimensional harmonic crystal with disorder

We study the problem of heat conduction in a mass-disordered two-dimensional harmonic crystal. Using two different stochastic heat baths, we perform simulations to determine the system size (L) dependence of the heat current (J). For white noise heat baths we find that J ~ 1/L^a with $a \approx 0.59$ while correlated noise heat baths gives $a \approx 0.51$. A special case with correlated disorder is studied analytically and gives a=3/2 which agrees also with results from exact numerics.Comment: Revised version. 4 pages, 3 figure

A new approach to the study of the ground-state properties of 2D Ising spin glass

A new approach known as flat histogram method is used to study the +/-J Ising spin glass in two dimensions. Temperature dependence of the energy, the entropy, and other physical quantities can be easily calculated and we give the results for the zero-temperature limit. For the ground-state energy and entropy of an infinite system size, we estimate e0 = -1.4007 +/- 0.0085 and s0 = 0.0709 +/- 0.006, respectively. Both of them agree well with previous calculations. The time to find the ground-states as well as the tunneling times of the algorithm are also reported and compared with other methods.Comment: 11 pages, 4 figure

Flat histogram simulation of lattice polymer systems

We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as end-to-end distance or radius of gyration can be easily calculated using this method. Ground-state energy can also be determined. We also explore the accuracy and limitations of this method. Key words: Monte Carlo algorithms, flat histogram sampling, HP model, lattice polymer systemsComment: 7 RevTeX two-column page

Identification of a Blood-Based Protein Biomarker Panel for Lung Cancer Detection

Lung cancer is the deadliest cancer worldwide, mainly due to its advanced stage at the time of diagnosis. A non-invasive method for its early detection remains mandatory to improve patients’ survival. Plasma levels of 351 proteins were quantified by Liquid Chromatography-Parallel Reaction Monitoring (LC-PRM)-based mass spectrometry in 128 lung cancer patients and 93 healthy donors. Bootstrap sampling and least absolute shrinkage and selection operator (LASSO) penalization were used to find the best protein combination for outcome prediction. The PanelomiX platform was used to select the optimal biomarker thresholds. The panel was validated in 48 patients and 49 healthy volunteers. A 6-protein panel clearly distinguished lung cancer from healthy individuals. The panel displayed excellent performance: area under the receiver operating characteristic curve (AUC) = 0.999, positive predictive value (PPV) = 0.992, negative predictive value (NPV) = 0.989, specificity = 0.989 and sensitivity = 0.992. The panel detected lung cancer independently of the disease stage. The 6-protein panel and other sub-combinations displayed excellent results in the validation dataset. In conclusion, we identified a blood-based 6-protein panel as a diagnostic tool in lung cancer. Used as a routine test for high- and average-risk individuals, it may complement currently adopted techniques in lung cancer screening.publishedVersio

Real-world sustained minimal residual disease (MRD) negativity using NGS in multiple myeloma.

e19280 Background: MRD assessment has been increasingly incorporated into guidelines and routine care for patients (pts) with multiple myeloma (MM). It has been widely shown that pts who achieve deep MRD negativity (MRD-) have longer PFS/OS. Clinical guidelines now include sustained MRD- (two consecutive MRD- results; (10−5, 12 mo. apart) as a response criterion. . NGS MRD (clonoSEQ; Adaptive Biotechnologies; Seattle, WA) is the only FDA authorized method for bone-marrow MRD assessment in MM. A large longitudinal database of quantitative NGS MRD values from routine patient care now enables real-world analysis. We used our data to provide insight into testing patterns and sustained MRD-. Methods: The population included internal data of NGS MRD clinical samples from Jan 2018 to Jan 2020. We examined MRD- achievement overall and sustained MRD- as defined by guidelines. For pts who achieved sustained MRD- and had subsequent MRD testing, we examined if they remained in an MRD- state. Results: We identified 1,675 pts with MM who had ≥1 MRD tests after baseline Clonality (ID) assessment. The age/sex distribution (med. age = 65; 58% male) was consistent with epidemiologic data. 837 (49.9%) and 541 (32.2%) achieved MRD- at 10−5 or 10−6 thresholds, respectively. Of the 190 pts with ≥2 MRD tests at least 12 mos. apart, 82 (43.2%) and 45 (23.7%) had sustained MRD- at 10−5 and 10−6 thresholds, respectively. Of 82 pts who achieved 12 mo. sustained MRD- at 10−5, 15 had a subsequent MRD test, of which all remained MRD-. Of 45 pts who achieved 12 mo. sustained negativity at 10−6, 4 had a subsequent MRD test, of which all remained MRD-. Conclusions: We believe this represents one of the earliest real-world study examining NGS MRD attainment of sustained MRD- defined by guidelines. It is notable that many pts reached deep MRD negativity, with a significant percentage having sustained MRD negativity meet guideline-defined criteria. Long-term follow-up and incorporation of clinical parameters &amp; outcomes data will enable further insights from this real-world dataset. [Table: see text] </jats:p