Platelet accumulation under high shear rates at the site of atherosclerotic plaque rupture leads to myocardial infarction and stroke. Current antiplatelet therapies remain ineffective within a large percentage of the population, while presenting significant risks for bleeding. We explore a novel way to inhibit arterial thrombus formation by biophysical means without the use of platelet inactivating drugs. Our computational multi-scale dynamics model has predicted that charged particles of a specific size may entangle von Willebrand Factor (vWF) polymers and reduce the amount of elongation at high shear rates. We tested this hypothesis experimentally for negatively charged nanoparticles (CNP) to inhibit arterial thrombus formation. CNP of a particular size and charge inhibited thrombus formation, with a 10-fold peak inhibition over control conditions of thrombotic occlusion. Particles of differing material composition, size, and charge had little effect as predicted by computational studies. Surprisingly, the dose response curve was not sigmoidal, but exhibited a peak at 1.5 CNP:vWF proteins, which was not predicted by the model. This study describes a new antithrombotic agent that may have a different mechanism of action than current pharmaceutical therapies.