The Beam Lifetime 3 (BL3) experiment at the National Institute of Standards and Technology, USA, aims to improve the precision of neutron lifetime measurements and will hopefully resolve the inconsistency between beam and bottle measurements of the neutron lifetime by enhancing the precision of this beam measurement. In the BL3 experiment, where protons from neutron decay are detected in a silicon detector, a GEANT4-based simulation was used to model, develop, and optimize the experimental setup. The physics list, used to simulate particle transportation and interactions, was derived from one of the advanced examples of GEANT4 and extended with a screened nuclear recoil model appropriate for low-energy proton-nucleus scattering of protons in silicon. This approach will allow the many applications of the SRIM (Stopping and Range of Ions in Matter) software for modelling these interactions to be expanded into the much more general GEANT4 framework where nuclear and other effects can be included. By using the example in TestEm7/StandardNR, G4BL3/SNR, and the physics list in GEANT4, the energy deposition and backscattering/ transmission of 35 keV protons on a silicon detector are studied. Comparing the outcomes with SRIM and confirming the energy accumulation in GEANT4's numerous processes and its effects on the ratio of various components are being analyzed.